Skip to main content
NCBI home page
UKPMC Funders Author Manuscripts logoLink to UKPMC Funders Author Manuscripts
. Author manuscript; available in PMC: 2026 Mar 18.
Published in final edited form as: Structure. 2025 Aug 12;33(10):1643–1648.e1. doi: 10.1016/j.str.2025.07.014

Cryo-EM structure of the vault from human brain reveals symmetry mismatch at its caps

Sofia Lövestam 1,2,*, Sjors HW Scheres 1
PMCID: PMC7618893  EMSID: EMS212831  PMID: 40803316

Abstract

The vault protein is expressed in most eukaryotic cells, where it is assembled on polyribosomes into large hollow barrel-shaped complexes. Despite its widespread and abundant presence in cells, the biological function of the vault remains unclear. In this study, we describe the cryo-EM structure of vault particles that were imaged as a contamination of a preparation to extract tau filaments from brain tissue of an individual with progressive supranuclear palsy (PSP). We identify a mechanism of symmetry mismatch at the caps of the vault, from 39-fold to 13-fold symmetry, where two out of three monomers are sequentially excluded from the cap, resulting in a narrow, greasy pore at the tip of the vault. Our structure offers valuable insights for engineering carboxy-terminal modifications of the major vault protein (MVP) for potential therapeutic applications.

Graphical abstract.

Graphical abstract

Open in a new tab

Introduction

The vault, first identified in 1986 by electron microscopy (EM) as a contaminant in clathrin-coated vesicle preparations from rat liver, is an abundant, hollow, barrel-like macromolecular complex found in the cytoplasm of nearly all eukaryotic cells.1,2 Vault particles are among the largest known macromolecular complexes in the cell: they measure approximately 41 × 41 × 72 nm and have a molecular weight of ~13 MDa. The structure of the shell of the vault was first solved by X-ray crystallography3 and subsequently by cryo-EM single-particle analysis.4,5 It consists of two symmetrically packed half-vaults, each formed by 39 copies of the major vault protein (MVP), a 100 kDa protein that consists of 12 domains: nine N-terminal structural repeats (R1–R9), a shoulder or SPFH domain, a cap helix, and a carboxy-terminal cap-ring domain. In both X-ray and cryo-EM structures,3,4 the application of 39-fold symmetry reduced the information available about the structure at the top and bottom caps of the vault, where there is insufficient space to accommodate 39 monomers.6

The function of the vault remains unknown. The protein shell has been reported to encapsulate vPARP (193 kDa),7 telomerase associated protein-1 TEP1 (240 kDa),8 and a small untranslated RNA (vault RNA) of 141 bases.1 The vault has been found to be expressed more highly in cancerous cells9,10 and has been suggested to play a role as toxin remover. Elevated levels of MVP have implicated the vault in the development of multidrug resistance in (MDR) in various cancers.11,12

The large size and non-immunogenic properties of the vault makes it an attractive vehicle for bioengineering approaches to delivering a diverse range of molecules into cells. The amino-terminus of the MVP is situated at the waist of the vault, where it embeds into the lumen (i.e., the interior of the vault); the carboxy-terminus extends outwards at the cap.4 Both termini have been engineered to facilitate targeted delivery and encapsulation of therapeutic compounds. Incorporating additional amino acids at the carboxy-terminus enables the display of targeting peptides on the vault surface, promoting specific interactions with cell surface receptors. For instance, recombinant vaults with engineered carboxy-terminal extensions have been shown to bind to epithelial cells directly or via a monoclonal antibody targeting the epidermal growth factor receptor (EGFR).13 Additionally, it has been shown that introducing an amphipathic α-helix at the amino-terminus of the MVP (i.e., in the lumen of the vault) creates a microenvironment that is suitable for encapsulating hydrophobic compounds and thereby enhances the delivery of lipophilic drugs into cells.14

We regularly observe vaults particles in cryo-EM images of amyloid filaments that we extract from human brain tissue with neuro-degenerative disease using sarkosyl solubilization and ultracentrifugation. Here, we calculate a cryo-EM reconstruction using vault particle images in cryo-EM micrographs of brain extracts from an individual with progressive supranuclear palsy (PSP), which we had previously deposited in the EMPIAR database (EMPIAR-1076515). Using symmetry expansion and focused image classification techniques in RELION,16 we reveal how the 39-fold symmetry at the caps of the vault is broken by the sequential exclusion of two MVP monomers, leading to a narrow pore on each cap of the vault that comprises only 13 MVP monomers. This structure could be engineered for targeted drug delivery.

Results

Cryo-EM micrographs of brain extracts from an individual with PSP15 showed multiple vault particles, most of which contained internal density and some of which were empty (Figure 1A, scale bar, 50 nm). We predominantly observed intact vaults but occasionally also detected half-vaults, in accordance with previous reports.4

Figure 1. Cryo-EM of the vault particle.

Figure 1

Open in a new tab

(A) Cryo-EM micrograph of vault particles. Pink arrows indicate vaults; green arrows are PSP filaments and orange arrows are ferritin particles. Scale bar, 50 nm.

(B) Electron density map of the vault.

Using D39 symmetry, we determined the structure of the vault complex at an overall resolution of 3.1 Å (STAR Methods; Figure 1B; Extended Data Figure 1A). Albeit at higher resolution, our D39 structure is nearly identical to previously reported structures of the vault in the primed state.4 We used the D39 map to build an atomic model for the majority of the MVP residues (11–803), which comprise the structural repeats (R1–R9), the shoulder domain, and the cap helix domain (Figure 2). Lower local resolution (4.0 Å) for the first three repeats (R1–R3) suggests the presence of unresolved structural heterogeneity at the waist of the vault. We did not observe density for the first eleven residues of MVP, nor for any molecules that might be encapsulated within the vault. As with previously reported structures of the vault, the reconstructed density at the caps was smeared, which precluded atomic modeling of the carboxy-terminal residues 801–893.

Figure 2. Cap of the vault.

Figure 2

Open in a new tab

(A) Top view of the vault. Cryo-EM density is shown for the central region of the cap; a cartoon model is shown fitted into the density.

(B) Side view of the parallel β-barrel formed by 26 MVP subunits.

(C and D)(C) Top view of the pore showing the exclusion of monomer (A) (in purple) and (D) as in (B) but as a side view.

(E) Close-ups of monomers (A, B, and C) (left to right). Monomers A are shown in purple; monomers B in pink; and monomers C in green.

To improve the reconstructed density at the cap of the vault, we used D39 symmetry expansion, followed by two rounds of focused 3D classification in C13 symmetry on one of the caps (see STAR Methods). This procedure resulted in a map with a resolution of 3.6 Å that shows three distinct arrangements of MVP monomers, where two out of every three MVP monomers are sequentially excluded from the cap structure.

In the monomer that is excluded first (monomer A; purple in Figure 2), the long α helix that spans residues 803–823 in the other two monomers breaks at residue 813, and the chain folds toward the lumen, where residues 815–826 form another short α helix. In the other two monomers (monomers B and C; green and pink in Figure 2), following the long α helix that comprises residues 803–823, the chains transition into β strands that comprise residues 829–834 and that form a 26-membered parallel β-barrel, with a diameter of 38 Å and with all chains pointing down toward the center of the vault.

The monomer that is excluded second (monomer B; green in Figure 2), then forms a small loop and a short α helix, comprising residues 835–853, that packs against the outside of the 26-membered parallel β-barrel, and below the long α helices formed by residues 803–823 of monomers B and C.

Finally, at the center of the cap, the cryo-EM density becomes too smeary to identify the position of residues beyond D834 for monomer C. However, weaker density in this region suggests that the carboxy-terminal residues of monomer C may fold back upwards, forming what is possibly a second parallel β-barrel-like pore with 13 β-strands and a diameter of 16 Å. It is possible that the weak cryo-EM density in this central pore is a consequence of variations in the specific residues that make up this pore. Based on the amino acid sequence of MVP, residues at both the inside and outside of this barrel are likely to be of a hydrophobic nature (Figure 4). This greasy pore may adopt multiple orientations with respect to the wider 26-membered parallel β-barrel, which also forms a hydrophobic ring made by residues L831 and I832 (Figures 3 and 4).

Figure 4. Structure and sequence of the 13-subunit pore.

Figure 4

Open in a new tab

(A) Cross-sectional view of the central portion of the vault cap. The vault structure is shown as a cartoon, and the unmodelled density is shown in orange.

(B) Primary sequence of the vault spanning residues 834–893. Putative residues which line the pore are shown with their one-letter code in two possible arrangements. Hydrophobic residues are highlighted in orange.

Figure 3. Hydrophobic features at the cap of the vault.

Figure 3

Open in a new tab

(A) Top view of the vault model with unmodeled density highlighted in orange.

(B) Hydrophobicity plot showing a hydrophobic ring made by residues L381 and I382 on the inside of the 26-membered parallel β-barrel. The central unmodeled density is indicated by an orange dashed circle.

(C) Cross-sectional view of the pore hydrophobicity plot.

Discussion

Although the vault is among the largest known protein complex and MVP is of high abundance and conservation in eukaryotes, its function remains a mystery. Nevertheless, a better understanding of the structure of the vault is of importance for engineering these complexes for the delivery of therapeutics, as encapsulation of cargo within the vault’s protein shell could potentially bypass the immune system for the delivery of immunogenic therapeutics.17

Previous studies were unable to resolve the cap of the vault and instead hypothesized that the monomers cross over and form a double-layered cap to accommodate the 39 MVP chains.18 Our cryo-EM reconstruction now reveals that the 39-fold symmetry is broken by the sequential exclusion of two out of every three monomers from the cap structure. Our density for the region closest to the central axis of the vault still does not support atomic modeling, probably due to remaining conformational heterogeneity that we were unable to resolve in our image processing. Weaker density in this region of the map suggests that an inner pore is made by a 13-stranded β-barrel. The same 13-stranded β-barrel was also observed in the structure of a vault complex that was purified from rat liver, which was reported as a preprint19 during the review of this manuscript and after we posted our manuscript as a preprint.20 A comparable mechanism has been observed in the Erlin1/2 complex, which is composed of 13 subunits of Erlin1 and 13 subunits of Erlin2, forming a 26-mer “half-vault” barrel that sits on the membrane of the endoplasmic reticulum. At the cap of the Erlin1/2 complex, Erlin2 is selectively excluded, resulting in a 13-stranded β-barrel formed exclusively by Erlin1.21 Given the hydrophobic nature of the residues in the corresponding part of the MVP sequence, the 13-stranded β-barrel at the vault cap is likely to have a greasy interior, which would favor the passing of hydrophobic molecules, or preclude the passing of polar or charged molecules. Modification of this part of the MVP sequence to residues of a different chemical nature could be used to make this pore selective for different types of molecules entering the vault. Furthermore, we were unable to resolve any internal densities within the vault. The vault is known to encapsulate TEP1, PARP4, and vRNA. A recent preprint describes how the fourth amino-terminal repeat of MVP interacts specifically with PARP4, and that incorporation of PARP4 in the vault affects both cargo selection and the subcellular localization of the vault.22 While questions regarding the function of the vault remain to be deciphered, our structure will inform bioengineering approaches that seek to alter which molecules pass through its cap, or approaches that aim to place signals on the cap that target it toward specific cell types. Furthermore, the mechanism of symmetry mismatch identified in this study implies that any modification to the carboxy-terminal residues of MVP will remain inside the lumen of the vault for two out of every three monomers.

Resource Availability

Lead contact

Further information and requests for resources and reagents should be directed to and will be fulfilled by the lead contact, Sofia Lövestam (lovestam@mrc-lmb.cam.ac.uk).

Materials availability

This study did not generate new unique reagents.

Star★Methods

Key Resources Table

REAGENT or RESOURCE SOURCE IDENTIFIER
Deposited data
Cryo-EM micrographs Iudin et al.23 EMPIAR: 10765
Entire vault: Cryo-EM 3D reconstruction This paper EMDB: EMD-53805
Vault cap: Cryo-EM 3D reconstruction This paper EMDB: EMD-53806
Entire vault: atomic coordinates This paper PDB: 9R86
Vault cap: atomic coordinates This paper PDB: 9R87
Software and algorithms
ChimeraX version 1.4 Pettersen et al.24 https://www.cgl.ucsf.edu/chimerax
RELION version 5 Kimanius et al.25 https://relion.readthedocs.io/en
ISOLDE Croll26 https://tristanic.github.io/isolde/
Open in a new tab

Method Details

Cryo-EM image processing

Cryo-EM micrographs were downloaded from EMPIAR23 (accession code 1076515) and processed in RELION25 (Extended Data Figure 2). Movies were motion corrected using RELION’s implementation of MotionCor2, and Contrast Transfer Function (CTF) parameters were estimated using CTFFIND-4.1.27 Manually picked vault particles from 50 micrographs were used to train a Topaz28 model to pick the remaining 3561 micrographs. Auto-picked particles were extracted in a box size of 640 Å and a pixel size of 5.75 Å. Reference-free 2D classification was used to assess the quality of the picking and showed the presence of views from multiple directions. Selecting 2D class averages with vault particles, we re-extracted 17,202 particles with a box size of 735.8 Å and a pixel size of 1.30 Å. Subsequent 3D auto-refinement in D39 symmetry and starting from an angular sampling rate of 1.8° was performed using a published vault cryo-EM map (EMDB 1347829), low-pass filtered to 60 Å, as an initial model. 3D classification was used to remove suboptimal particles, resulting in a dataset of 7,367 particles that were used for a final 3D refinement with D39 symmetry and CTF refinement.30 Standard post-processing procedures in RELION were used to obtain a sharpened map with a resolution of 3.1 Å.

To improve the reconstructed density at the cap of the vault, and without yet knowing the true symmetry of the cap, we used D39 symmetry expansion of the particles from the final 3D auto-refinement, resulting in 574,626 expanded particles. We then performed focused 3D classification with partial signal subtraction31 of the rest of the vault density on one of the caps, with ten classes, imposing C13 symmetry, and without further optimisation of the particle poses from the refinement in D39 symmetry. We selected 129,211 expanded particles that belonged to two of the classes that showed clear structures with 13-fold symmetry at the center of the cap. The map of the second class was rotated −360°/39 with respect to the map of the first class. The remaining 445,415 particles were subjected to a second round of 3D focused classification into ten classes, which identified another 48,584 particles that showed clear structures with 13-fold symmetry at the center of the cap. This map was rotated +360°/39 with respect to the map of the first class from the first round of focused classification. Two half-maps of the cap structure were then reconstructed using the relion_re-construct program from the original half-sets of the combined 177,795 expanded particles, imposing C13 symmetry and using the original poses from the 3D refinement with D39 symmetry (while modifying the first Euler (rot) angles of the two rotated classes by ±360°/39). Standard RELION post-processing yielded a final map of the cap structure to an estimated resolution of 3.6 Å.

Model building

The model in the map with D39 symmetry was rebuilt from PDB entry 4hl8.4 The model for the cap of the vault was built using ModelAngelo.32 Both models were refined in ISOLDE.26 The map and model with D39 symmetry and for the cap of the vault were deposited in the PDB and EMDB and are available under accession codes 9R86, 9R87 and 53805, 53806, respectively.

Quantification And Statistical Analysis

Model building and refinement statistics are summarised in Table 1.4

Table 1. Model validation.

Data processing Entire vault PDB: 9R86 EMDB: 53805 Vault cap PDB: 9R87 EMDB: 53806
Initial particle images (no.) 24760 574626
Final particle images (no.) 7367 65387
Symmetry imposed D39 C13
Map resolution FSC 0.143 (Å) 3.1 3.6
Refinement
Initial model used (PDB code) 4hL8 ModelAngelo
Model resolution FSC 0.5 (Å) 3.7 4.1
Map sharpening B factor (Å2) –76 –98
Model composition
    Non-hydrogen atoms 220,580 20,605
    Protein residues 27,651 2704
    Ligands na na
B factors (Å2)
    Protein 95.61 96.82
    Ligand na na
R.m.s. deviations
    Bond lengths (Å) 0.011 0.010
    Bond angles (?) 1.932 1.873
Validation
    MolProbity score 0.74 0.84
    Clashscore 0.13 0.07
    Poor rotamers (%) 0.25 0.62
Ramachandran plot
    Favored (%) 96.89 95.58
    Allowed (%) 3.11 4.30
    Disallowed (%) 0 0.11
Open in a new tab

Supplementary Material

Supplemental information can be found online at https://doi.org/10.1016/j.str.2025.07.014.

Document S1
Document S2

In brief.

Lövestam and Scheres present a cryo-EM structure of vault particles, found during tau filament extraction from progressive supranuclear palsy (PSP) brain tissue. They reveal a symmetry shift at the vault cap, offering new insights into vault architecture and potential strategies for engineering vault proteins for therapeutic applications.

Highlights.

  • Vault protein is a large barrel-shaped protein in most eukaryotic cells

  • Cryo-EM reveals structure of human vault protein from brain tissue

  • We reveal a mechanism of symmetry mismatch at the vault’s caps

  • The structure provides insight for future bioengineering efforts

Acknowledgments

We thank Max Wilkinson and David Li for their enthusiasm surrounding the mysteries of the vault protein; Toby Darling, Ivan Clayson, and Jake Grimmett for assistance with high-performance computing; and Leonard Rome for critical reading of the manuscript. S.L. is grateful to Anne Bertolotti for encouragement to work on proteins that are not related to her project. This work was supported by the MRC, as part of the UK Research and Innovation (UKRI) (MC_UP_A025_1013 to S.H.W.S.).

Footnotes

Author Contributions

S.L. and S.H.W.S. both analyzed cryo-EM data and jointly wrote the manuscript.

Declaration Of Interests

The authors declare no competing interests.

Data code and code availability

  • Cryo-EM micrographs can be downloaded from EMPIAR under the accession code 10765.23 The cryo-EM maps for the vault have been deposited in the EMDB under accession codes 53805 and 53806 and the atomic models under the accession codes 9R86 and 9R87. They are publicly available as of the date of publication.

  • This paper does not report any original code.

  • Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.

References

  • 1.Kedersha NL, Rome LH. Isolation and characterization of a novel ribonucleoprotein particle: large structures contain a single species of small RNA. J Cell Biol. 1986;103:699–709. doi: 10.1083/jcb.103.3.699. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 2.Kedersha NL, Miquel MC, Bittner D, Rome LH. Vaults. II. Ribonucleoprotein structures are highly conserved among higher and lower eukaryotes. J Cell Biol. 1990;110:895–901. doi: 10.1083/jcb.110.4.895. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 3.Tanaka H, Kato K, Yamashita E, Sumizawa T, Zhou Y, Yao M, Iwasaki K, Yoshimura M, Tsukihara T. The Structure of Rat Liver Vault at 3.5 Angstrom Resolution. Science. 2009;323:384–388. doi: 10.1126/science.1164975. [DOI] [PubMed] [Google Scholar]
  • 4.Guerra P, González-Alamos M, Llauró A, Casañas A, Querol-Audí J, de Pablo PJ, Verdaguer N. Symmetry disruption commits vault particles to disassembly. Sci Adv. 2022;8:eabj7795. doi: 10.1126/sciadv.abj7795. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 5.Ding K, Zhang X, Mrazek J, Kickhoefer VA, Lai M, Ng HL, Yang OO, Rome LH, Zhou ZH. Solution Structures of Engineered Vault Particles. Structure. 2018;26:619–626.:e3. doi: 10.1016/j.str.2018.02.014. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 6.Casañas A, Querol-Audí J, Guerra P, Pous J, Tanaka H, Tsukihara T, Verdaguer N, Fita I. New Features of Vault Architecture and Dynamics Revealed by Novel Refinement Using the Deformable Elastic Network Approach. Acta Crystallogr D Biol Crystallogr. 2013:1054–1061. doi: 10.1107/S0907444913004472. [DOI] [PubMed] [Google Scholar]
  • 7.Kickhoefer VA, Siva AC, Kedersha NL, Inman EM, Ruland C, Streuli M, Rome LH. The 193-kD vault protein, VPARP, is a novel poly(ADP-ribose) polymerase. J Cell Biol. 1999;146:917–928. doi: 10.1083/jcb.146.5.917. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 8.Kickhoefer VA, Stephen AG, Harrington L, Robinson MO, Rome LH. Vaults and telomerase share a common subunit, TEP1. J Biol Chem. 1999;274:32712–32717. doi: 10.1074/jbc.274.46.32712. [DOI] [PubMed] [Google Scholar]
  • 9.Berger W, Spiegl-Kreinecker S, Buchroithner J, Elbling L, Pirker C, Fischer J, Micksche M. Overexpression of the human major vault protein in astrocytic brain tumor cells. Int J Cancer. 2001;94:377–382. doi: 10.1002/ijc.1486. [DOI] [PubMed] [Google Scholar]
  • 10.Scheffer GL, Schroeijers AB, Izquierdo MA, Wiemer EA, Scheper RJ. Lung resistance-related protein/major vault protein and vaults in multidrug-resistant cancer. Curr Opin Oncol. 2000;12:550–556. doi: 10.1097/00001622-200011000-00007. [DOI] [PubMed] [Google Scholar]
  • 11.Kickhoefer VA, Rajavel KS, Scheffer GL, Dalton WS, Scheper RJ, Rome LH. Vaults are up-regulated in multidrug-resistant cancer cell lines. J Biol Chem. 1998;273:8971–8974. doi: 10.1074/jbc.273.15.8971. [DOI] [PubMed] [Google Scholar]
  • 12.Lötsch D, Steiner E, Holzmann K, Spiegl-Kreinecker S, Pirker C, Hlavaty J, Petznek H, Hegedus B, Garay T, Mohr T, et al. Major vault protein supports glioblastoma survival and migration by upregulating the EGFR/PI3K signalling axis. Oncotarget. 2013;4:1904–1918. doi: 10.18632/oncotarget.1264. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 13.Kickhoefer VA, Han M, Raval-Fernandes S, Poderycki MJ, Moniz RJ, Vaccari D, Silvestry M, Stewart PL, Kelly KA, Rome LH. Targeting Vault Nanoparticles to Specific Cell Surface Receptors. ACS Nano. 2009;3:27–36. doi: 10.1021/nn800638x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 14.Buehler DC, Marsden MD, Shen S, Toso DB, Wu X, Loo JA, Zhou ZH, Kickhoefer VA, Wender PA, Zack JA, Rome LH. Bioengineered vaults: Self-assembling protein shell-lipophilic core nanoparticles for drug delivery. ACS Nano. 2014;8:7723–7732. doi: 10.1021/nn5002694. JPEG. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 15.Shi Y, Zhang W, Yang Y, Murzin AG, Falcon B, Kotecha A, van Beers M, Tarutani A, Kametani F, Garringer HJ, et al. Structure-based classification of tauopathies. Nature. 2021;598:359–363. doi: 10.1038/s41586-021-03911-7. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 16.Nakane T, Kimanius D, Lindahl E, Scheres SH. Characterisation of molecular motions in cryo-EM single-particle data by multi-body refinement in RELION. eLife. 2018;7:e36861. doi: 10.7554/eLife.36861. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 17.Rome LH, Kickhoefer VA. Development of the Vault Particle as a Platform Technology. ACS Nano. 2013;7:889–902. doi: 10.1021/nn3052082. [DOI] [PubMed] [Google Scholar]
  • 18.Anderson DH, Kickhoefer VA, Sievers SA, Rome LH, Eisenberg D. Draft Crystal Structure of the Vault Shell at 9-Å Resolution. PLoS Biol. 2007;5:e318. doi: 10.1371/journal.pbio.0050318. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 19.Li H, Vallese F, Clarke OB. The vault particle is enclosed by a C13-symmetric cap with a positively charged exterior. bioRxiv. 2025;2025:658390. doi: 10.1126/sciadv.adz6794. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 20.Lövestam S, Scheres HW. Cryo-EM structure of the vault from human brain reveals symmetry mismatch at its caps. bioRxiv. 2025;2025:656403. doi: 10.1016/j.str.2025.07.014. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 21.Gao J, Sherpa D, Kupko N, Shao S. Structures of human organellar SPFH protein complexes. bioRxiv. 2025;2025:649849. doi: 10.1038/s41467-025-65078-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 22.Lodwick JE, Shen R, Erramilli S, Xie Y, Roganowicz K, Kossiakoff AA, Zhao M. Structural Insights into the Roles of PARP4 and NAD+ in the Human Vault Cage. bioRxiv. 2024;2024:601040. doi: 10.1038/s41467-025-61981-x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 23.Iudin A, Korir PK, Salavert-Torres J, Kleywegt GJ, Patwardhan A. EMPIAR: a public archive for raw electron microscopy image data. Nat Methods. 2016;13:387–388. doi: 10.1038/nmeth.3806. [DOI] [PubMed] [Google Scholar]
  • 24.Pettersen EF, Goddard TD, Huang CC, Meng EC, Couch GS, Croll TI, Morris JH, Ferrin TE. UCSF ChimeraX: Structure visualization for researchers, educators, and developers. Protein Sci. 2021;30:70–82. doi: 10.1002/pro.3943. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 25.Kimanius D, Dong L, Sharov G, Nakane T, Scheres SHW. New tools for automated cryo-EM single-particle analysis in RELION-4.0. Biochem J. 2021;478:4169–4185. doi: 10.1042/BCJ20210708. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 26.Croll TI. ISOLDE : a physically realistic environment for model building into low-resolution electron-density maps. Acta Crystallogr D Struct Biol. 2018;74:519–530. doi: 10.1107/S2059798318002425. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 27.Rohou A, Grigorieff N. CTFFIND4: Fast and accurate defocus estimation from electron micrographs. J Struct Biol. 2015;192:216–221. doi: 10.1016/j.jsb.2015.08.008. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 28.Bepler T, Morin A, Rapp M, Brasch J, Shapiro L, Noble AJ, Berger B. Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs. Nat Methods. 2019;16:1153–1160. doi: 10.1038/s41592-019-0575-8. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 29.Turner J, Abbott S, Fonseca N, Pye R, Carrijo L, Duraisamy AK, Salih O, Wang Z, Kleywegt GJ, Morris KL, et al. EMDB-the Electron Microscopy Data Bank. Nucleic Acids Res. 2024;52:D456–D465. doi: 10.1093/nar/gkad1019. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 30.Zivanov J, Nakane T, Scheres SHW. Estimation of high-order aberrations and anisotropic magnification from cryo-EM data sets in RELION-3.1. IUCrJ. 2020;7:253–267. doi: 10.1107/S2052252520000081. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 31.Bai XC, Fernandez IS, McMullan G, Scheres SHW. Ribosome structures to near-atomic resolution from thirty thousand cryo-EM particles. eLife. 2013;2:e00461. doi: 10.7554/eLife.00461. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 32.Jamali K, Käll L, Zhang R, Brown A, Kimanius D, Scheres SHW. Automated model building and protein identification in cryo-EM maps. Nature. 2024;628:450–457. doi: 10.1038/s41586-024-07215-4. [DOI] [PMC free article] [PubMed] [Google Scholar]

Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Document S1
EMS212831-supplement-Document_S1.pdf (2.2MB, pdf)
Document S2
EMS212831-supplement-Document_S2.pdf (24.7MB, pdf)

Data Availability Statement

  • Cryo-EM micrographs can be downloaded from EMPIAR under the accession code 10765.23 The cryo-EM maps for the vault have been deposited in the EMDB under accession codes 53805 and 53806 and the atomic models under the accession codes 9R86 and 9R87. They are publicly available as of the date of publication.

  • This paper does not report any original code.

  • Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.

RESOURCES