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. 2018 Feb 24;10(2):677–686. doi: 10.1007/s12551-018-0402-y

Structural atlas of dynein motors at atomic resolution

Akiyuki Toda 1,2, Hideaki Tanaka 1,2, Genji Kurisu 1,2,✉
PMCID: PMC5899744  PMID: 29478092

Abstract

Dynein motors are biologically important bio-nanomachines, and many atomic resolution structures of cytoplasmic dynein components from different organisms have been analyzed by X-ray crystallography, cryo-EM, and NMR spectroscopy. This review provides a historical perspective of structural studies of cytoplasmic and axonemal dynein including accessory proteins. We describe representative structural studies of every component of dynein and summarize them as a structural atlas that classifies the cytoplasmic and axonemal dyneins. Based on our review of all dynein structures in the Protein Data Bank, we raise two important points for understanding the two types of dynein motor and discuss the potential prospects of future structural studies.

Keywords: Dynein, Dynein subunits, Axonemal dynein light chain-1, Molecular motor, Structural analysis

Introduction

Dyneins are microtubule (MT)-based molecular motors that perform diverse biological functions (Roberts et al. 2013). They work as large multiple bio-nanomachines (> 1 MDa) consisting of a heavy chain (HC), intermediate chain (IC), light intermediate chain (LIC), and light chain (LC). The HC possesses ATPase activity and provides the driving force for power generation to conduct a wide variety of cellular functions. The other chains are involved in regulating the HC and are therefore called accessary chains. Dyneins are classified as either cytoplasmic or axonemal on the basis of their physiological function and cellular localization, and there is a clear distinction between the two types. Cytoplasmic dyneins serve as power generators for migration and intracellular transport, whereas axonemal dyneins are located in the axoneme and are responsible for ciliary/flagellar beating. Complete genome analysis of several organisms has revealed that there are at least 15 HC genes present in most organisms; two of which encode cytoplasmic dyneins, while the others encode axonemal ones.

The structural analysis of dynein motors began with the LCs with relatively smaller molecular weights and then progressed to the larger chains, such as ICs and HCs (Table 1). The first HC structure to be published was that of dynein-c (Burgess et al. 2003), which is an isoform of an axonemal dynein purified from a green alga, Chlamydomonas reinhardtii. Although the resolution of the negatively stained electron microscopy (EM) images was not sufficient to build the atomic coordinates, the first model of the dynein power stroke was proposed from the two different EM structures with and without nucleotide. However high-resolution structural information on the HC, which is crucial to understand the molecular mechanism of the mechano-chemical coupling of dynein motors, was long awaited.

Table 1.

Structures of cytoplasmic dynein available in the PDB

PDB ID Dynein component Complex Organism Method Res. (Å) References
Heavy chain
3ERR Cytoplasmic dynein 1 heavy chain 1 MTBD–SRS chimera Mus musculus X-ray 2.27 Carter et al. 2008
3J67 Dynein motor domain Strongylocentrotus purpuratus EM 34.00 Lin et al. 2014
3J68 Dynein motor domain Strongylocentrotus purpuratus EM 30.00 Lin et al. 2014
3J1T Cytoplasmic dynein 1 heavy chain 1 MTBD–SRS chimera–MT complex Mus musculus EM 9.70 Redwine et al. 2012
3J1U Cytoplasmic dynein 1 heavy chain 1 MTBD–SRS chimera–MT complex Mus musculus EM 9.70 Redwine et al. 2012
3J6P Dynein heavy chain, cytoplasmic Dynein MTBD–MT complex Dictyostelium discoideum EM 8.20 Uchimura et al. 2015
3QMZ Cytoplasmic dynein heavy chain Saccharomyces cerevisiae X-ray 6.00 Carter et al. 2011
3AY1 Dynein heavy chain, cytoplasmic Dynein motor domain–ADP Dictyostelium discoideum X-ray 4.50 Kon et al. 2011
3VKG Dynein heavy chain, cytoplasmic Dynein motor domain–ADP Dictyostelium discoideum X-ray 2.81 Kon et al. 2012
3VKH Dynein heavy chain, cytoplasmic Dynein motor domain–ADP Dictyostelium discoideum X-ray 3.80 Kon et al. 2012
3WUQ Cytoplasmic dynein 1 heavy chain 1 Mus musculus X-ray 3.50 Nishikawa et al. 2014
4AI6 Dynein heavy chain, cytoplasmic Dynein motor domain–GST chimera–ADP Saccharomyces cerevisiae X-ray 3.40 Schmidt et al. 2012
4AKG Dynein heavy chain, cytoplasmic Dynein motor domain–GST chimera–ATP Saccharomyces cerevisiae X-ray 3.30 Schmidt et al. 2012
4AKH Dynein heavy chain, cytoplasmic Dynein motor domain–GST chimera–AMPPNP Saccharomyces cerevisiae X-ray 3.60 Schmidt et al. 2012
4AKI Dynein heavy chain, cytoplasmic Dynein motor domain–GST chimera–LuAc derivative Saccharomyces cerevisiae X-ray 3.70 Schmidt et al. 2012
4RH7 Cytoplasmic dynein 2 heavy chain 1 GFP–Cytoplasmic dynein 2 heavy chain 1 synthetic construct Homo sapiens X-ray 3.41 Schmidt et al. 2014
4W8F Dynein heavy chain, cytoplasmic Dynein heavy chain–lysozyme chimera Saccharomyces cerevisiae. Enterobacteria phase t4 sensu lato X-ray 3.54 Bhabha et al. 2014
5AFR Dynein heavy chain, cytoplasmic Saccharomyces cerevisiae X-ray 5.00 Urnavicius et al. 2015
5AFU Cytoplasmic dynein Dynein tail–dynactin–BICD2 complex Sus scrofa EM Urnavicius et al. 2015
5AYH Cytoplasmic dynein 1 heavy chain 1 Mus musculus X-ray 3.01 Nishikawa et al. 2016
5NUG Cytoplasmic dynein 1 heavy chain 1 Homo sapiens EM 3.80 Zhang et al. 2017
5NVS Cytoplasmic dynein 1 heavy chain 1 Dynein tail–IC–RobI–LIC–LC8–TcTex complex Homo sapiens EM 8.40 Zhang et al. 2017
5NVU Cytoplasmic dynein 1 heavy chain 1 Phi-particle conformation Homo sapiens EM 15.00 Zhang et al. 2017
5NW4 Cytoplasmic dynein 1 heavy chain 1 Dynactin–BICD2 complex Homo sapiens EM 8.70 Zhang et al. 2017
5VH9 Dynein heavy chain, cytoplasmic Dynein heavy chain–Lis1 complex Saccharomyces cerevisiae EM 7.70 DeSantis et al. 2017
5VLJ Dynein heavy chain, cytoplasmic Dynein heavy chain–Lis1 complex Saccharomyces cerevisiae EM 10.50 DeSantis et al. 2017
Light intermediate chain
4W7G Dynein light intermediate chain Chaetomium thermophilum X-ray 2.10 Schroeder et al. 2014
Light chain
 LC8
1CMI Dynein light chain 1, cytoplasmic LC8–PIN complex Homo sapiens X-ray 2.50 Liang et al. 1999
1F3C Dynein light chain 1, cytoplasmic Rattus norvegicus NMR – Fan et al. 2001
1F95 Dynein light chain 1, cytoplasmic DLC8–BIM peptide complex Rattus norvegicus NMR – Fan et al. 2001
1F96 Dynein light chain 1, cytoplasmic DLC8–NNOS peptide complex Rattus norvegicus NMR – Fan et al. 2001
1RE6 Dynein light chain 2, cytoplasmic Mus musculus NMR – Day et al. 2004
1RHW Dynein light chain 1, cytoplasmic Drosophila melanogaster NMR – Makokha et al. 2004
1PWJ Dynein light chain 2, cytoplasmic Rattus norvegicus NMR – Wang et al. 2003
1PWK Dynein light chain 2, cytoplasmic Rattus norvegicus NMR – Wang et al. 2003
1Y4O Dynein light chain roadblock-type 1 Mus musculus NMR – Song et al. 2005
1YO3 Dynein light chain 1, putative Plasmodium falciparum X-ray 1.65 Vedadi et al. 2007
1Z09 Dynein light chain roadblock-type 1 Homo sapiens NMR – Ilangovan et al. 2005
2B95 Dynein light chain roadblock-type 1 Homo sapiens NMR –
2E8J Dynein light chain roadblock-type 1 Homo sapiens NMR –
2HZ5 Dynein light chain roadblock-type 1 Homo sapiens X-ray 2.10 Liu et al. 2006
2P2T Dynein light chain 1, cytoplasmic LC8–IC74 peptide complex Drosophila melanogaster X-ray 3.00 Benison et al. 2007
2XQQ Dynein light chain 2, cytoplasmic DYNLL2–peptide complex Homo sapiens X-ray 1.31 Rapali et al. 2011
3BRI Dynein light chain 1, cytoplasmic Drosophila melanogaster X-ray 1.70 Benison et al. 2008
3BRL Dynein light chain 1, cytoplasmic LC8(S88E) –Swa peptide complex Drosophila melanogaster X-ray 1.90
3DVH Dynein light chain 1, cytoplasmic K36P mutant Drosophila melanogaster X-ray 2.00 Lightcap et al. 2008
3DVP Dynein light chain 1, cytoplasmic LC8–Pak1 peptide complex Drosophila melanogaster X-ray 2.50 Lightcap et al. 2008
3DVT Dynein light chain 1, cytoplasmic Drosophila melanogaster X-ray 2.30 Lightcap et al. 2008
3E2B Dynein light chain 1, cytoplasmic LC8–Swallow peptide complex Drosophila melanogaster X-ray 2.00 Benison et al. 2008
3GLW Dynein light chain 1, cytoplasmic IC–LC8 complex Drosophila melanogaster X-ray 3.15 Hall et al. 2009
3P8M Dynein light chain 2, cytoplasmic DYNLL2–GCN4 complex Homo sapiens X-ray 2.90 Rapali et al. 2011
3RJS Dynein light chain motor protein Toxoplasma gondii X-ray 1.50 Qureshi et al. 2013
3ZKE Dynein light chain 1, cytoplasmic LC8–Nek9 peptide complex Homo sapiens X-ray 2.20 Gallego et al. 2013
3ZKF Dynein light chain 1, cytoplasmic LC8–Nek9 peptide complex Homo sapiens X-ray 2.60 Gallego et al. 2013
4D07 Dynein light chain 2, cytoplasmic Dynll2–Myosin 5A tail complex Homo sapiens X-ray 1.85 Bodor et al. 2014
4DS1 Dynein light chain 1, cytoplasmic Dyn2–Nup159 complex Saccharomyces cerevisiae X-ray 1.85 Romes et al. 2012
4HT6 Dynein light chain 1, cytoplasmic Dyn2–Pac11 complex Saccharomyces cerevisiae X-ray 1.90 Rao et al. 2013
4QH7 Dynein light chain 1, cytoplasmic LC8-Ana2(159–168) complex Drosophila melanogaster X-ray 1.83 Slevin et al. 2014
4QH8 Dynein light chain 1, cytoplasmic LC8–Ana2(237–246) complex Drosophila melanogaster X-ray 1.90 Slevin et al. 2014
5E0L Dynein light chain 1, cytoplasmic LC8 (DLC1, DYNLL)–Chica (415–424) complex Drosophila melanogaster X-ray 1.31 Clark et al. 2016
5E0M Dynein light chain 1, cytoplasmic LC8 (DLC1, DYNLL)–Chica (468–476) complex Drosophila melanogaster X-ray 1.65 Clark et al. 2016
5WOF Dynein light chain 1, putative Plasmodium falciparum X-ray 1.65 Vedadi et al. 2007
 TcTex-1
1YGT Dynein light chain TcTex-type Drosophila melanogaster X-ray 1.70 Williams et al. 2005
5HXL dynein light chain TcTex-1 Magnaporthe oryzae X-ray 1.97
5JPW Dynein light chain TcTex-type 1 TcTex1–IC2 complex Homo sapiens NMR – Merino-Gracia et al. 2016
 LC7/RobI
3L7H Dynein light chain roadblock Drosophila melanogaster X-ray 1.95
3L9K Dynein light chain roadblock RE64145p–IC complex Drosophila melanogaster X-ray 3.00
 Lis1
1UUJ Platelet-activating factor acetylhydrolase IB subunit alpha Mus musculus X-ray 1.75 Kim et al. 2004
1VYH Platelet-activating factor acetylhydrolase IB subunit beta Lis1–PAF–AH complex Mus musculus X-ray 3.40 Tarricone et al. 2004
Complex
2PG1 (Dynein light chain 1, cytoplasmic, Dynein light chain TcTex-type, Cytoplasmic dynein 1 intermediate chain 2 LC8–TcTex1–IC Drosophila melanogaster X-ray 2.80 Williams et al. 2007
3FM7 Dynein light chain 1, cytoplasmic, Dynein light chain TcTex-type, Cytoplasmic dynein 1 intermediate chain IC–TcTex-1–LC8 complex Drosophila melanogaster X-ray 3.50 Hall et al. 2009
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IC intermediate, LC light chain, MT microtubule, MTBD MT-binding domain

Since the establishment of a method for producing functional recombinant cytoplasmic dynein motor domains (Nishiura et al. 2004), X-ray crystallographic high-resolution structures have been reported that describe detailed structural elements, such as the N-terminal linker, AAA+ (ATPases associated with various cellular activities) ring, stalk/strut coiled coils with the microtubule binding domain (MTBD), and the C-terminal non-AAA structure named “C-sequence,” as well as revealing the structural changes that occur upon ATP hydrolysis (Carter et al. 2008, 2011, Kon et al. 2011, 2012; Schmidt et al. 2012). Most recently, a single-particle cryogenic electron microscopy (cryo-EM) structure of a vast complex of cytoplasmic dynein 1 bound to dynactin and an N-terminal construct of BICD2 (total molecular mass, 1.4 MDa) has been reported (Zhang et al. 2017).

To date, many structures of cytoplasmic dynein components from different organisms have been analyzed by X-ray crystallography, cryo-EM, and NMR spectroscopy (Tables 1 and 2). As the number of solved structures of cytoplasmic dynein increases year by year, the information is becoming too complex to assess the accumulated structural data at a glance (Table 1). By contrast, only four atomic structures of axonemal dynein are available in the Protein Data Bank (Table 2) (Mullen et al. 2000; Wu et al. 2003; Kato et al. 2014).

Table 2.

Structures of axonemal dynein available in the PDB

PDB ID Dynein component Complex Organism Method Res. (Å) References
Heavy chain
 2RR7 Dynein heavy chain 9 Chlamydomonas reinhardtii NMR – Kato et al. 2014
Light chain
 LC1
  1DS9 Dynein light chain 1, axonemal Chlamydomonas reinhardtii NMR – Mullen et al. 2000
  1M9L Dynein light chain 1, axonemal Chlamydomonas reinhardtii NMR – Wu et al. 2003
  5YXM Dynein light chain 1, axonemal Chlamydomonas reinhardtii X-ray 1.55 this study
TcTex-1
 1XDX Dynein light chain TcTex1 Chlamydomonas reinhardtii NMR – Wu et al. 2005
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In this short article, we review representative structural studies of the components that classify cytoplasmic and axonemal dyneins and summarize them as a structural atlas (Fig. 1) with additional updated structural data on LC1 from C. reinhardtii obtained by ourselves (Fig. 2).

Fig. 1.

Fig. 1

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Structural atlas of cytoplasmic dynein. a Schematic diagram of the cytoplasmic dynein complex. b Superposition of solved dynein structures on the schematic diagram. Atomic structures at a resolution of 4 Å or higher are shown. From left to right, pre-power stroke (dark gray) and post-power stroke (light gray) structures of the dynein motor domain, LIS1 (red), LIC (green), IC (navy) with Robl (cyan), LC8 (orange), and TcTex (yellow) are shown

Fig. 2.

Fig. 2

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Currently available atomic structures of axonemal dynein. a Crystal structure of LC1 (PDB ID: 5YXM). LC1 crystals were grown at 4 °C via the sitting-drop vapor diffusion method by mixing 200 nL of LC1 (20 mg/mL protein) with an equal volume of reservoir solution (0.1 M ammonium phosphate monobasic, 10% (w/v) PEG3,350). LC1 crystals were soaked in cryo-protectant solution (0.1 M ammonium phosphate monobasic, 35% (w/v) PEG3,350, 10 mM Tris-HCl (pH 8.0), 100 mM NaCl) overnight, and then flash-cooled in liquid nitrogen. The X-ray diffraction experiment was performed on beamline BL44XU, SPring-8, Harima Japan. The collected images were processed by using HKL2000 software (Otwinowski and Minor 1997). Molecular replacement and refinement were performed by using Phenix (Adams et al. 2002) and COOT (Emsley and Cowtan 2004). TLS parameters were analyzed by using the TLSMD server (Painter and Merritt 2006), and 12 TLS groups were introduced in the subsequent refinement. The final structure was validated by using MolProbity (Lovell et al. 2003). The detailed crystallographic statistics information can be available in the PDB (https://pdbj.org/mine/summary/5yxm). The ribbon diagram of LC1 is shown in green. b Superposition of the X-ray (green) and NMR (magenta) structures of LC1. A representative NMR structure is shown (PDB ID: 1M9L). c Amino acid sequence alignment of LC1 with secondary structure assignments. d Superposition of the X-ray structure with anisotropic B factors and main chain conformation of the NMR structure (magenta). e NMR structure of the MTBD of dynein-c (PDB ID: 2RR7). The additional flap structure which is an insertion sequence in the MTBD of the axonemal dynein is shown in orange

Light chain

Many structures of LCs from different organisms have been reported, including LC7, LC8, TcTex-1, and Lis1 (Table 1). It is thought that the LCs are important for dynein–cargo interactions. Several structures of LC8 (also called DYNLL or dynein light chain 1) have been determined as a complex with peptides derived from binding partners by X-ray crystallography and NMR (Table 1, Fig. 1). Details of the molecular function of LC8 remain unknown, but Chlamydomonas cells of a LC8 deletion mutant lack retrograde intraflagellar transport and display short deficient flagella (Pazour et al. 1998).

Axonemal dynein light chain-1 (LC1) in C. reinhardtii (DNAL1 in Homo sapiens), whose structure has been solved by NMR spectroscopy (Mullen et al. 2000; Wu et al. 2003) (Fig. 2), is a component of outer arm dynein (OAD) (Table 2). Knockdown of LC1 has been found to reduce beat frequency in the flatworm planarian (Rompolas et al. 2010), and the expression of an LC1 mutant shows dominant-negative effects on swimming velocity and beat frequency in C. reinhardtii (Patel-King and King 2009). These observations suggest that LC1 acts as a regulator to beat cilia/flagella. Originally, LC1 was thought to be directly bound to tubulins and to tether the OADγ HC to the microtubule (Patel-King and King 2009). Furthermore, it has been widely assumed that LC1 associates with AAA1 and AAA3 or AAA4 of the AAA+ ring in the gamma heavy chain of OAD (OADγ) in C. reinhardtii (Benashski et al. 1999). However, it was recently reported that LC1 is tightly bound to the MTBD of OADγ, which is located at the tip of stalk region in the motor domain (Ichikawa et al. 2015). This was the first report of an LC interacting with the MTBD. Moreover, it was also discovered that the binding of LC1 to the MTBD decreases the MT-binding affinity of the HC (Ichikawa et al. 2015). Because it has been reported that the ATPase activity of the HC is increased in the presence of MTs (Kon et al. 2009), both results imply that LC1 indirectly changes the ATPase activity of OADγ and regulates ciliary/flagellar beating. However, the molecular mechanism that tunes ATPase activity through the MTBD still remains poorly understood.

Although NMR structures of LC1 are available, we determined the X-ray structure of LC1 at 1.55-Å resolution to enable a more detailed discussion (Fig. 2a). As expected from a comparison of the amino acid sequences and NMR structures of LC1 (Benashski et al. 1999; Mullen et al. 2000; Wu et al. 2003), the crystal structure of LC1 shows a leucine-rich repeat conformation. However, there are large conformational differences between the X-ray and NMR structures, especially in the N- and C- terminal regions and the crystal structure differs from the NMR structures at the secondary structure level (Fig. 2b, c). In particular, the differences in the secondary structure between the X-ray and NMR structures are surprisingly large at Ala22–Glu24 and Met182–Val184 in the N-terminal and C-terminal regions, respectively (Fig. 2c). These results suggest that these two terminal regions may play the role of flexible hinges and that large conformational differences may be induced when LC binds to its partner proteins.

We also analyzed the anisotropic temperature factors of the X-ray structure with reference to the main chain conformation of the NMR structures (Fig. 2d). There were significant correlations between the anisotropic directions of the temperature factors and the structural differences between the X-ray and NMR structures, which implies that the intrinsic flexibility of LC1 is manifested in the structural discrepancy between X-ray and NMR structures.

Light intermediate chain

The LIC subunit is present in cytoplasmic dynein, but not in axonemal dynein (Inaba 2007). There are three LIC homologs in H. sapiens: LIC1, LIC2, and LIC3. On the one hand, LIC1 and LIC2 are associated with cytoplasmic dynein 1 (Hughes et al. 1995) and are thought to play important roles in cargo transport and stability of the HC (Trokter et al. 2012). On the other hand, LIC3 interacts with cytoplasmic dynein 2 (Grissom et al. 2002). Sequence analysis indicates that the LICs are divided into two domains: a conserved N-terminal domain and the other domain. The only known structure of LIC is the structure of the conserved N-terminal domain of LIC from a thermophilic hyphal fungus, Chaetomium thermophilum (Schroeder et al. 2014). Although the structure shows a Ras-like G-protein fold, the nucleotide pocket is empty. Biochemical experiments confirmed that this fungus LIC does not bind nucleotide, whereas human LIC1 does bind nucleotides (Schroeder et al. 2014). To clarify the differences in LICs by species and isoform, further structural studies and biochemical experiments will be needed.

Intermediate chain

There are four IC homologs in H. sapiens. DYNC1I1 (cytoplasmic IC1) and DYNC1I2 (cytoplasmic IC2) associate with cytoplasmic dynein HC, while DNAI1 (axonemal IC1) and DNAI2 (axonemal IC2) interact with axonemal HCs. All IC homologs possess a conserved WD40 domain in the C-terminus that interacts with HCs (Tynan et al. 2000). A secondary structure analysis using Jpred and RONN predicted that the N-terminal region of cytoplasmic IC1 and IC2 comprise coiled coil and highly disordered regions (Williams et al. 2012). However, the secondary structure prediction analysis also indicated that the N-terminal region of IC1 is highly disordered but that of IC2 possesses a folded structure in axonemal ICs (Williams et al. 2012).

In terms of atomic structure, so far, there is no high-resolution structure of either the whole IC or its WD40 domain (Tables 1 and 2). However, crystal structures of TcTex1 and LC8 with IC peptides containing the interaction sites for LCs have been determined and explain how IC interacts with LCs (Williams et al. 2007; Hall et al. 2009). Moreover, the whole structure of a cytoplasmic dynein complex determined by cryo-EM has revealed the structural arrangement of IC within the cytoplasmic dynein complex (Zhang et al. 2017). However, the precise site of the IC–HC interaction remains unclear due to the low resolution. Thus, more work is needed to gain structural insights into the dynein ICs.

Heavy chain

The HC is the largest polypeptide of the dynein complex and contains the motor domain, which is the minimum component needed for ATP-dependent motor activity. In 2008, Carter and colleagues determined the first crystal structure of the MTBD of an HC fused to the seryl–tRNA synthetase (SRS) from Thermus thermophilus (Carter et al. 2008). Several years later, a more complete structure of the stalk coiled coil with the MTBD was reported by our group (Nishikawa et al. 2014, 2016). Since then, many crystal structures of the cytoplasmic dynein motor domain in different nucleotide states have been determined (Carter et al. 2011; Kon et al. 2011, 2012, Schmidt et al. 2012, 2014; Bhabha et al. 2014). According to these structures, the HC is composed of multiple functional units, including the tail, linker, AAA+ ring, stalk/strut, and C-sequence. Each unit possesses distinct functions to drive force generation in the motor. In addition to X-ray crystallography, cryo-EM has more recently revealed the structure of a cytoplasmic dynein complex including the HC, IC, LIC, and LC, both alone and together with dynactin–BICD2 (DDB) (Zhang et al. 2017). The cryo-EM structures have revealed the relative arrangement of the cytoplasmic dynein components in an inhibitory state and provide insights into how cytoplasmic dynein is inhibited and activated.

In contrast to the genes encoding cytoplasmic dynein HCs, those encoding axonemal dyneins are many and diverse. The arrangement of the HC and the characteristics of the motor activity along the MT differ completely between axonemal dynein and cytoplasmic dynein. Cytoplasmic dyneins work as a dimer, whereas the functional oligomeric states of axonemal dynein HCs include monomers, dimers, and trimers. Moreover, an MT gliding assay has revealed that some axonemal dyneins display clockwise translocation of MTs (Kikushima and Kamiya 2008; Yamaguchi et al. 2015). These findings indicate that axonemal dyneins are highly diverse proteins in terms of the functional properties of their HCs. Among the axonemal dynein HCs, only the NMR structure of the MTBD of dynein-c from C. reinhardtii has been determined so far (Kato et al. 2014) (Fig. 2e). As compared with cytoplasmic dynein, the molecular mechanism underlying the motor activities of axonemal dyneins remains relatively unclear. Clearly, structural and functional studies of axonemal dynein HCs need to be addressed as soon as possible.

Conclusions and future prospects

Dynein motors are biologically important bio-nanomachines. In parallel with recent developments in structural biology, such as single-particle cryo-EM and synchrotron-based X-ray nano-crystallography, more and more fascinating three-dimensional structures of dyneins have become available. Based on the survey of the structures available at atomic resolutions shown above, we would like to point out two important directions for future research. One is the imbalance in structural information between cytoplasmic and axonemal dynein. Atomic data are very much focused on cytoplasmic dyneins and remarkably less structural work on axonemal dyneins has been reported. The oligomeric states of axonemal dyneins are so diverse that each dynein is likely to have a specific structural role. The expansion of structural information on axonemal dyneins is greatly anticipated.

The second point is that structures of dynein on MTs are lacking. This point is important because the dynein that walks along the MT is really the functional molecule. For the other cytoskeletal motors, kinesin and myosin, not only structures in different nucleotide states but also structures in complex with the α, β-tubulin dimer or actin filament have been reported. Two structures of the dynein MTBD and MT complex have been solved by cryo-EM using a helical averaging technique (Table 1), one of which was done by a collaborative team including one of the authors. However, the resolutions of the two structures are 9.7 and 8.2 Å, and only flexible docking based on the available crystal structures is applicable at those resolutions. In 2014, Imai and his colleagues reported the structure of dynein walking on MTs using engineered chimeric dynein construct (Imai et al. 2015), but the resolution is not high enough to discuss the structure at the residue level. We await with impatience a high-resolution structure of dynein walking on MTs.

Acknowledgements

We thank the staff of the beamline BL44XU at SPring-8, Japan, for the help during data collection and Prof. Toshiki Yagi for providing the plasmid used in this study.

Funding information

This work was supported by a Grant-in-Aid for Scientific Research B (JP26291014) from the Japan Society for the Promotion of Science (JSPS) and JSPS Fellows Number JP17J07553.

Compliance with ethical standards

Conflict of interest

Akiyuki Toda declares that he has no conflict of interest. Hideaki Tanaka declares that he has no conflict of interest. Genji Kurisu declares that he has no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Footnotes

This article is part of a Special Issue on “Biomolecules to Bio-nanomachines - Fumio Arisaka 70th Birthday” edited by Damien Hall, Junichi Takagi, and Haruki Nakamura.

References

  1. Adams PD, Grosse-Kunstleve RW, Hung LW, Loerger TR, McCoy AJ, Moriarty NW, Reed RJ, Sacchettini JC, Sauter NK, Terwilliger TC. PHENIX: Building new software for automated crystallographic structure determination. Acta Crystallogr D Biol Crystallogr. 2002;58:1948–1954. doi: 10.1107/S0907444902016657. [DOI] [PubMed] [Google Scholar]
  2. Benashski SE, Patel-King RS, King SM. Light chain 1 from the Chlamydomonas outer dynein arm is a leucine-rich repeat protein associated with the motor domain of the gamma heavy chain. Biochemistry. 1999;38:7253–7264. doi: 10.1021/bi990466y. [DOI] [PubMed] [Google Scholar]
  3. Benison G, Karplus PA, Barbar E. Structure and dynamics of LC8 complexes with KXTQT-motif peptides: swallow and dynein intermediate chain compete for a common site. J Mol Biol. 2007;371:457–468. doi: 10.1016/j.jmb.2007.05.046. [DOI] [PubMed] [Google Scholar]
  4. Benison G, Karplus PA, Barbar E. The interplay of ligand binding and quaternary structure in the diverse interactions of dynein light chain LC8. J Mol Biol. 2008;384:954–966. doi: 10.1016/j.jmb.2008.09.083. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Bhabha G, Cheng HC, Zhang N, et al. Allosteric communication in the dynein motor domain. Cell. 2014;159:857–868. doi: 10.1016/j.cell.2014.10.018. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Bodor A, Radnai L, Hetényi C, et al. DYNLL2 dynein light chain binds to an extended linear motif of myosin 5a tail that has structural plasticity. Biochemistry. 2014;53:7107–7122. doi: 10.1021/bi500574z. [DOI] [PubMed] [Google Scholar]
  7. Burgess SA, Walker ML, Sakakibara H, et al. Dynein structure and power stroke. Nature. 2003;421:715–718. doi: 10.1038/nature01377. [DOI] [PubMed] [Google Scholar]
  8. Carter AP, Cho C, Jin L, Vale RD. Crystal structure of the dynein motor domain. Science. 2011;331(80):1159–1165. doi: 10.1126/science.1202393. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Carter AP, Garbarino JE, Wilson-Kubalek EM, et al. Structure and functional role of dynein’s microtubule-binding domain. Science. 2008;322:1691–1695. doi: 10.1126/science.1164424. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Clark S, Nyarko A, Löhr F, et al. The anchored flexibility model in LC8 motif recognition: insights from the Chica complex. Biochemistry. 2016;55:199–209. doi: 10.1021/acs.biochem.5b01099. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Day CL, Puthalakath H, Skea G, et al. Localization of dynein light chains 1 and 2 and their pro-apoptotic ligands. Biochem J. 2004;377:597–605. doi: 10.1042/bj20031251. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. DeSantis ME, Cianfrocco MA, Htet ZM, et al. Lis1 has two opposing modes of regulating cytoplasmic dynein. Cell. 2017;170:1197–1208.e12. doi: 10.1016/j.cell.2017.08.037. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Emsley P, Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr. 2004;60:2126–2132. doi: 10.1107/S0907444904019158. [DOI] [PubMed] [Google Scholar]
  14. Fan J-S, Zhang Q, Tochio H, et al (2001) Structural basis of diverse sequence-dependent target recognition by the 8 kDa dynein light chain11 Edited by P. E. Wright. J Mol Biol 306:97–108. doi: 10.1006/jmbi.2000.4374 [DOI] [PubMed]
  15. Gallego P, Velazquez-Campoy A, Regue L, et al. Structural analysis of the regulation of the DYNLL/LC8 binding to Nek9 by phosphorylation. J Biol Chem. 2013;288:12283–12294. doi: 10.1074/jbc.M113.459149. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Grissom PM, Vaisberg EA, McIntosh JR. Identification of a novel light intermediate chain (D2LIC) for mammalian cytoplasmic dynein 2. Mol Biol Cell. 2002;13:817–829. doi: 10.1091/mbc.01-08-0402. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Hall J, Karplus PA, Barbar E. Multivalency in the assembly of intrinsically disordered dynein intermediate chain. J Biol Chem. 2009;284:33115–33121. doi: 10.1074/jbc.M109.048587. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Hughes SM, Vaughan KT, Herskovits JS, Vallee RB. Molecular analysis of a cytoplasmic dynein light intermediate chain reveals homology to a family of ATPases. J Cell Sci. 1995;108(Pt 1):17–24. doi: 10.1242/jcs.108.1.17. [DOI] [PubMed] [Google Scholar]
  19. Ichikawa M, Saito K, Yanagisawa H-A, et al. Axonemal dynein light chain-1 locates at the microtubule-binding domain of the γ heavy chain. Mol Biol Cell. 2015;26:4236–4247. doi: 10.1091/mbc.E15-05-0289. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Ilangovan U, Ding W, Zhong Y, et al. Structure and dynamics of the homodimeric dynein light chain km23. J Mol Biol. 2005;352:338–354. doi: 10.1016/j.jmb.2005.07.002. [DOI] [PubMed] [Google Scholar]
  21. Imai H, Shima T, Sutoh K, et al. Direct observation shows superposition and large scale flexibility within cytoplasmic dynein motors moving along microtubules. Nat Commun. 2015;6:8179. doi: 10.1038/ncomms9179. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Inaba K (2007) Molecular basis of sperm flagellar axonemes: structural and evolutionary aspects. In: Annals of the New York Academy of Sciences. pp 506–526 [DOI] [PubMed]
  23. Kato YS, Yagi T, Harris SA, et al. Structure of the microtubule-binding domain of flagellar dynein. Structure. 2014;22:1628–1638. doi: 10.1016/j.str.2014.08.021. [DOI] [PubMed] [Google Scholar]
  24. Kikushima K, Kamiya R. Clockwise translocation of microtubules by flagellar inner-arm dyneins in vitro. Biophys J. 2008;94:4014–4019. doi: 10.1529/biophysj.107.123083. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Kim MH, Cooper DR, Oleksy A, et al. The structure of the N-terminal domain of the product of the lissencephaly gene Lis1 and its functional implications. Structure. 2004;12:987–998. doi: 10.1016/j.str.2004.03.024. [DOI] [PubMed] [Google Scholar]
  26. Kon T, Imamula K, Roberts AJ, et al. Helix sliding in the stalk coiled coil of dynein couples ATPase and microtubule binding. Nat Struct Mol Biol. 2009;16:325–333. doi: 10.1038/nsmb.1555. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Kon T, Oyama T, Shimo-Kon R, et al. The 2.8 Å crystal structure of the dynein motor domain. Nature. 2012;484:345–350. doi: 10.1038/nature10955. [DOI] [PubMed] [Google Scholar]
  28. Kon T, Sutoh K, Kurisu G. X-ray structure of a functional full-length dynein motor domain. Nat Struct Mol Biol. 2011;18:638–642. doi: 10.1038/nsmb.2074. [DOI] [PubMed] [Google Scholar]
  29. Liang J, Jaffrey SR, Guo W, et al. Structure of the PIN/LC8 dimer with a bound peptide. Nat Struct Biol. 1999;6:735–740. doi: 10.1038/11501. [DOI] [PubMed] [Google Scholar]
  30. Lightcap CM, Sun S, Lear JD, et al. Biochemical and structural characterization of the Pak1-LC8 interaction. J Biol Chem. 2008;283:27314–27324. doi: 10.1074/jbc.M800758200. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Lin J, Okada K, Raytchev M, et al. Structural mechanism of the dynein power stroke. Nat Cell Biol. 2014;16:479–485. doi: 10.1038/ncb2939. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Liu JF, Wang ZX, Wang XQ, et al. Crystal structure of human dynein light chain Dnlc2A: structural insights into the interaction with IC74. Biochem Biophys Res Commun. 2006;349:1125–1129. doi: 10.1016/j.bbrc.2006.08.161. [DOI] [PubMed] [Google Scholar]
  33. Lovell SC, Davis IW, Arendall WB, de Bakker PI, Word JM, Prisant MG, Richardwon JS, Richardson DC. Structure validation by Calpha geometry: phi, psi and Cbeta Deviation. Proteins. 2003;50:437–450. doi: 10.1002/prot.10286. [DOI] [PubMed] [Google Scholar]
  34. Makokha M, Huang YJ, Montelione G, et al. The solution structure of the pH-induced monomer of dynein light-chain LC8 from Drosophila. Protein Sci. 2004;13:727–734. doi: 10.1110/ps.03462204. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Merino-Gracia J, Zamora-Carreras H, Bruix M, Rodríguez-Crespo I. Molecular basis for the protein recognition specificity of the dynein light chain DYNLT1/Tctex1. J Biol Chem. 2016;291:20962–20975. doi: 10.1074/jbc.M116.736884. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Mullen GP, King SM, Wu H, et al. Solution structure of a dynein motor domain associated light chain. Nat Struct Biol. 2000;7:575–579. doi: 10.1038/76804. [DOI] [PubMed] [Google Scholar]
  37. Nishikawa Y, Inatomi M, Iwasaki H, Kurisu G. Structural change in the dynein stalk region associated with two different affinities for the microtubule. J Mol Biol. 2016;428:1886–1896. doi: 10.1016/j.jmb.2015.11.008. [DOI] [PubMed] [Google Scholar]
  38. Nishikawa Y, Oyama T, Kamiya N, et al. Structure of the entire stalk region of the dynein motor domain. J Mol Biol. 2014;426:3232–3245. doi: 10.1016/j.jmb.2014.06.023. [DOI] [PubMed] [Google Scholar]
  39. Nishiura M, Kon T, Shiroguchi K, et al. A single-headed recombinant fragment of Dictyostelium cytoplasmic dynein can drive the robust sliding of microtubules. J Biol Chem. 2004;279:22799–22802. doi: 10.1074/jbc.M313362200. [DOI] [PubMed] [Google Scholar]
  40. Otwinowski Z, Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 1997;276:307–326. doi: 10.1016/S0076-6879(97)76066-X. [DOI] [PubMed] [Google Scholar]
  41. Painter J, Merritt EA. Optimal description of a protein structure in terms of multiple groups undergoing TLS motion. Acta Crystallogr D Biol Crystallogr. 2006;62:439–450. doi: 10.1107/S0907444906005270. [DOI] [PubMed] [Google Scholar]
  42. Patel-King RS, King SM. An outer arm dynein light chain acts in a conformational switch for flagellar motility. J Cell Biol. 2009;186:283–295. doi: 10.1083/jcb.200905083. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Pazour GJ, Wilkerson CG, Witman GB. A dynein light chain is essential for the retrograde particle movement of intraflagellar transport (IFT) J Cell Biol. 1998;141:979–992. doi: 10.1083/jcb.141.4.979. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Qureshi BM, Hofmann NE, Arroyo-Olarte RD, et al. Dynein light chain 8a of Toxoplasma gondii, a unique conoid-localized ß-strand-swapped homodimer, is required for an efficient parasite growth. FASEB J. 2013;27:1034–1047. doi: 10.1096/fj.11-180992. [DOI] [PubMed] [Google Scholar]
  45. Rao L, Romes EM, Nicholas MP, et al. The yeast dynein Dyn2-Pac11 complex is a dynein dimerization/processivity factor: structural and single-molecule characterization. Mol Biol Cell. 2013;24:2362–2377. doi: 10.1091/mbc.E13-03-0166. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Rapali P, Radnai L, Süveges D et al (2011) Directed evolution reveals the binding motif preference of the LC8/DYNLL hub protein and predicts large numbers of novel binders in the human proteome. PLoS One. 10.1371/journal.pone.0018818 [DOI] [PMC free article] [PubMed]
  47. Redwine WB, Hernandez-Lopez R, Zou S, et al. Structural basis for microtubule binding and release by dynein. Science. 2012;337(80):1532–1536. doi: 10.1126/science.1224151. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Roberts AJ, Kon T, Knight PJ, et al. Functions and mechanics of dynein motor proteins. Nat Rev Mol Cell Biol. 2013;14:713–726. doi: 10.1038/nrm3667. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Romes EM, Tripathy A, Slep KC. Structure of a yeast Dyn2-Nup159 complex and molecular basis for dynein light chain-nuclear pore interaction. J Biol Chem. 2012;287:15862–15873. doi: 10.1074/jbc.M111.336172. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. Rompolas P, Patel-King RS, King SM. An outer arm Dynein conformational switch is required for metachronal synchrony of motile cilia in planaria. Mol Biol Cell. 2010;21:3669–3679. doi: 10.1091/mbc.E10-04-0373. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. Schmidt H, Gleave ES, Carter AP. Insights into dynein motor domain function from a 3.3-Å crystal structure. Nat Struct Mol Biol. 2012;19:492–497. doi: 10.1038/nsmb.2272. [DOI] [PMC free article] [PubMed] [Google Scholar]
  52. Schmidt H, Zalyte R, Urnavicius L, Carter AP. Structure of human cytoplasmic dynein-2 primed for its power stroke. Nature. 2014;518:435–438. doi: 10.1038/nature14023. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. Schroeder CM, Ostrem JML, Hertz NT, Vale RD. A Ras-like domain in the light intermediate chain bridges the dynein motor to a cargo-binding region. Elife. 2014;3:e03351. doi: 10.7554/eLife.03351. [DOI] [PMC free article] [PubMed] [Google Scholar]
  54. Slevin LK, Romes EM, Dandulakis MG, Slep KC. The mechanism of dynein light chain LC8-mediated oligomerization of the Ana2 centriole duplication factor. J Biol Chem. 2014;289:20727–20739. doi: 10.1074/jbc.M114.576041. [DOI] [PMC free article] [PubMed] [Google Scholar]
  55. Song J, Tyler RC, Lee MS, et al. Solution structure of isoform 1 of Roadblock/LC7, a light chain in the dynein complex. J Mol Biol. 2005;354:1043–1051. doi: 10.1016/j.jmb.2005.10.017. [DOI] [PubMed] [Google Scholar]
  56. Tarricone C, Perrina F, Monzani S, et al. Coupling PAF signaling to dynein regulation: structure of LIS1 in complex with PAF-acetylhydrolase. Neuron. 2004;44:809–821. doi: 10.1016/j.neuron.2004.11.019. [DOI] [PubMed] [Google Scholar]
  57. Trokter M, Mucke N, Surrey T. Reconstitution of the human cytoplasmic dynein complex. Proc Natl Acad Sci. 2012;109:20895–20900. doi: 10.1073/pnas.1210573110. [DOI] [PMC free article] [PubMed] [Google Scholar]
  58. Tynan SH, Gee MA, Vallee RB. Distinct but overlapping sites within the cytoplasmic dynein heavy chain for dimerization and for intermediate chain and light intermediate chain binding. J Biol Chem. 2000;275:32769–32774. doi: 10.1074/jbc.M001537200. [DOI] [PubMed] [Google Scholar]
  59. Uchimura S, Fujii T, Takazaki H, et al. A flipped ion pair at the dynein-microtubule interface is critical for dynein motility and ATPase activation. J Cell Biol. 2015;208:211–222. doi: 10.1083/jcb.201407039. [DOI] [PMC free article] [PubMed] [Google Scholar]
  60. Urnavicius L, Zhang K, Diamant AG, et al. The structure of the dynactin complex and its interaction with dynein. Science. 2015;347:1441–1446. doi: 10.1126/science.aaa4080. [DOI] [PMC free article] [PubMed] [Google Scholar]
  61. Vedadi M, Lew J, Artz J, et al. Genome-scale protein expression and structural biology of plasmodium falciparum and related apicomplexan organisms. Mol Biochem Parasitol. 2007;151:100–110. doi: 10.1016/j.molbiopara.2006.10.011. [DOI] [PubMed] [Google Scholar]
  62. Wang W, Lo KWH, Kan HM, et al. Structure of the monomeric 8-kDa dynein light chain and mechanism of the domain-swapped dimer assembly. J Biol Chem. 2003;278:41491–41499. doi: 10.1074/jbc.M307118200. [DOI] [PubMed] [Google Scholar]
  63. Williams JC, Roulhac PL, Roy AG, et al. Structural and thermodynamic characterization of a cytoplasmic dynein light chain-intermediate chain complex. Proc Natl Acad Sci U S A. 2007;104:10028–10033. doi: 10.1073/pnas.0703614104. [DOI] [PMC free article] [PubMed] [Google Scholar]
  64. Williams JC, Siglin AE, Lightcap CM, Dawn A (2012) Structural analysis of dynein intermediate and light chains. In: Dyneins. pp 156–189
  65. Williams JC, Xie H, Hendrickson W a. Crystal structure of dynein light chain TcTex-1. J Biol Chem. 2005;280:21981–21986. doi: 10.1074/jbc.M414643200. [DOI] [PubMed] [Google Scholar]
  66. Wu H, Blackledge M, Maciejewski MW, et al. Relaxation-based structure refinement and backbone molecular dynamics of the dynein motor domain-associated light chain. Biochemistry. 2003;42:57–71. doi: 10.1021/bi026762j. [DOI] [PubMed] [Google Scholar]
  67. Wu H, Maciejewski MW, Takebe S, King SM. Solution structure of the Tctex1 dimer reveals a mechanism for dynein-cargo interactions. Structure. 2005;13:213–223. doi: 10.1016/j.str.2004.11.013. [DOI] [PubMed] [Google Scholar]
  68. Yamaguchi S, Saito K, Sutoh M, et al. Torque generation by axonemal outer-arm dynein. Biophys J. 2015;108:872–879. doi: 10.1016/j.bpj.2014.12.038. [DOI] [PMC free article] [PubMed] [Google Scholar]
  69. Zhang K, Foster HE, Rondelet A, et al. Cryo-EM reveals how human cytoplasmic dynein is auto-inhibited and activated. Cell. 2017;169:1303–1314.e18. doi: 10.1016/j.cell.2017.05.025. [DOI] [PMC free article] [PubMed] [Google Scholar]

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