Table 3:
Examples of integrative structures (shown in Figure 1).
| System name | Input data | Accession | Citation |
|---|---|---|---|
| INO80 | 17-Å resolution cryo-electron microscopy (EM) map, 212 intra-protein and 116 inter-protein cross-links | (Tosi et al., 2013) | |
| Polycomb Repressive Complex 2 (PRC2) | 21-Å resolution negative-stain EM map and ~60 intra-protein and inter-protein cross-links | (Ciferri et al., 2012)1 | |
| Large subunit of the mammalian mitochondrial ribosome (39S) | 4.9-Å resolution cryo-EM map and ~70 inter-protein cross-links | 4CE4 | (Greber et al., 2014b)2 |
| RNA polymerase II transcription pre-initiation complex | 16-Å resolution cryo-EM map plus 157 intra-protein and 109 inter-protein cross-links | (Murakami et al., 2013)3 | |
| Type III secretion system needle | 19.5-Å resolution cryo-EM map and solid-state nuclear magnetic resonance (NMR) data | 2LPZ | (Loquet et al., 2012)4 |
| Productive HIV-1 reverse transcriptase:DNA primer-template complex in the open educt state | Foerster resonance energy transfer (FRET) positioning and screening using a known HIV-1 reverse transcriptase structure | (Kalinin et al., 2012)2 | |
| HIV-1 capsid protein | Residual dipolar couplings and small-angle X-ray scattering (SAXS) data | 2M8L, 2M8N, 2M8P | (Deshmukh et al., 2013)5 |
| Human genome | Tethered chromosome conformation capture and population-based modeling | (Kalhor et al., 2011)6 | |
| Drosophila genome | Chromosome conformation capture and lamina DamID | (Li et al., 2017) | |
| α-globin gene domain | Chromosome Conformation Capture Carbon Copy (5C) | (Bau et al., 2011)7 | |
| Proteosomal lid | Native mass spectrometry and 28 cross-links | (Politis et al., 2014)8 | |
| ESCRT-I complex | SAXS, double electron-electron transfer, and FRET | (Boura et al., 2011) | |
| Actin together with the cardiac myosin binding protein C | Crystallographic and NMR structures of subunits and domains, with positions and orientations optimized against SAXS and small-angle neutron scattering data to reveal information about the quaternary interactions | (Whitten et al., 2008)9 | |
| [ΨCD]2 | Averaged cryo-electron tomography map, NMR | 2L1F | (Miyazaki et al., 2010) |
| Cyanobacterial circadian timing KaiB-KaiC complex | Hydrogen/deuterium exchange and collision cross-section data from mass spectrometry | (Snijder et al., 2014) | |
| Pre-pore and pore conformations of the pore-forming toxin aerolysin | Cryo-EM data and molecular dynamics simulations | (Degiacomi et al., 2013)10 | |
| A segment of a pleurotolysin pore map (~11 Å resolution); an ensemble of conformations shows the trajectory of β-sheet opening during pore formation | Cryo-EM, X-ray crystal subunit structures, fluorescence spectroscopy, cross-linking | 4V2T | (Lukoyanova et al., 2015)11 |
| Ternary complex of the iron-sulfur cluster assembly proteins desulfurase (orange) and scaffold protein Isu (blue) with a bacterial ortholog of frataxin (yellow) | NMR chemical shifts, SAXS, mutagenesis | (Prischi et al., 2010)12 | |
| SAGA transcription coactivator complex | 199 inter- and 240 intra-subunit cross-links, several comparative models based on X-ray crystal structures, and a transcription factor IID core EM map at 31 Å resolution | (Han et al., 2014)13 | |
| Bacterial (Thermus aquaticus) RNA polymerase-promoter open complex; subsequently validated by a crystal structure (Feng et al., 2016) | FRET | Mekler, 2002 #400} | |
| RNA ribosome-binding element from the turnip crinkle virus genome | NMR, SAXS, EM | DOI: 10.6084/m9.figshare.1295199 | (Gong et al., 2015)14 |
| Complex between RNA polymerase II and transcription factor IIF | Deposited crystal structure of RNA polymerase II, comparative models of some domains in transcription factor IIF and 95 intra-protein and 129 inter-protein cross-links | (Chen et al., 2010)15 | |
| Human and yeast TFIIH | XL-MS data, biochemical analyses, and previously published electron microscopy maps | (Luo et al., 2015) | |
| 40S-eIF1-eIF3 translation initiation complex | X-ray crystallography, EM, XL-MS | (Erzberger et al., 2014) | |
| ATP synthase membrane motor | cryo-EM (~7.8 Å resolution), XL-MS, and evolutionary couplings | (Leone and Faraldo-Gomez, 2016)16 | |
| 26S proteasome | 67 inter-protein and 26 intra-protein chemical cross-links in combination with EM maps | 5LN3 | (Wang et al., 2017) |
| Ino80 insert domain bound to the Rbv1/Rvb2 dodecamer | 12-Å resolution cryo-EM map, 226 chemical cross-links | (Zhou et al., 2017) | |
| Core of the yeast spindle pole body (SPB) | in vivo FRET, SAXS, X-ray crystallography, EM, two-hybrid analysis | (Viswanath et al., 2017a)2 | |
| E6AP/UBE3A-E6-p53 enzyme-substrate complex | XL-MS data of the complex with and without E6 | PDBDEV_00000022, PDBDEV_00000023 | (Sailer et al., 2018)17 |
| Nucleosome remodeler ISWI | XL-MS, SAXS, protein-protein docking | (Harrer et al., 2018) | |
| Urease activation complex | Mobility-mass spectrometry data | (Eschweiler et al., 2018) | |
| Chromosomal DNA organization | Super-resolution microscopy methods OligoSTORM and OligoDNA-PAINT, Hi-C data | (Nir et al., 2018)18 |
Figure panel reprinted from figure 11 of (Ciferri et al., 2012), used under the terms of the Creative Commons Attribution 3.0 license (https://creativecommons.org/licenses/by/3.0/).
Figure panel obtained via personal communication and used with permission of the author.
Panel from Figure 5 of (Murakami et al., 2013). Reprinted with permission from AAAS.
Figure 3 reprinted by permission from Springer Nature Terms and Conditions for RightsLink Permissions Springer Nature Customer Service Centre GmbH: Nature “Atomic model of the type III secretion system needle.” Loquet A, Sgourakis NG, Gupta R, Giller K, Riedel D, Goosmann C, Griesinger C, Kolbe M, Baker D, Becker S, Lange A. Copyright Springer Nature Publishing AG (2012).
Figure 9 reprinted (adapted) with permission from (Deshmukh et al., 2013). Copyright (2013) American Chemical Society.
Figure 6 reprinted by permission from Springer Nature Terms and Conditions for RightsLink Permissions Springer Nature Customer Service Centre GmbH: Nature Biotechnology “Genome architectures revealed by tethered chromosome conformation capture and population-based modeling.” Kalhor R, Tjong H, Jayathilaka N, Alber F, Chen L. Copyright Springer Nature Publishing AG (2012).
Figure 4 reprinted by permission from Springer Nature Terms and Conditions for RightsLink Permissions Springer Nature Customer Service Centre GmbH: Nature Structural & Molecular Biology “The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules.” Baù D, Sanyal A, Lajoie BR, Capriotti E, Byron M, Lawrence JB, Dekker J, Marti-Renom MA. Copyright Springer Nature Publishing AG (2011).
Figure 2 reprinted by permission from Springer Nature Terms and Conditions for RightsLink Permissions Springer Nature Customer Service Centre GmbH: Nature Methods “A mass spectrometry–based hybrid method for structural modeling of protein complexes.” Politis A, Stengel F, Hall Z, Hernández H, Leitner A, Walzthoeni T, Robinson CV, Aebersold R. Copyright Springer Nature Publishing AG (2014).
Copyright (2008) National Academy of Sciences.
Figure 6 reprinted by permission from Springer Nature Terms and Conditions for RightsLink Permissions Springer Nature Customer Service Centre GmbH: Nature Chemical Biology “Molecular assembly of the aerolysin pore reveals a swirling membrane-insertion mechanism.” Degiacomi MT, Iacovache I, Pernot L, Chami M, Kudryashev M, Stahlberg H, van der Goot FG, Dal Peraro M. Copyright Springer Nature Publishing AG (2013).
Figure 3 from (Lukoyanova et al., 2015) used under the terms of the Creative Commons Attribution 4.0 license (https://creativecommons.org/licenses/by/4.0/).
Figure 6 from (Prischi et al., 2010) used under the terms of the Creative Commons Attribution-NonCommercial-Share Alike 3.0 Unported License (https://creativecommons.org/licenses/by-nc-sa/3.0/).
Figure 7 from (Han et al., 2014) is Copyright (2014) Han Y, Luo J, Ranish J, Hahn S. EMBOpress.
Figure 3 from (Gong et al., 2015) used under the terms of the Creative Commons Attribution 4.0 license (https://creativecommons.org/licenses/by/4.0/).
Figure 4 from (Chen et al., 2010) used under the terms of the Creative Commons Attribution‐NonCommercial‐NoDerivs License (https://creativecommons.org/licenses/by-nc-nd/3.0/).
Figure 6 from (Leone and Faraldo-Gomez, 2016) used under the terms of the Creative Commons Attribution–Noncommercial–Share Alike 3.0 Unported license (https://creativecommons.org/licenses/by-nc-sa/3.0/).
Figure 4 from (Sailer et al., 2018) used under the terms of the Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/).
Figure 3 from (Nir et al., 2018) used under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/).