9Z5N | pdb_00009z5n

Cryo-EM structure of rabbit vault cap


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.25 Å
  • Aggregation State: TISSUE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9Z5N

This is version 1.1 of the entry. See complete history

Literature

The vault particle is enclosed by a C 13-symmetric cap with a positively charged exterior.

Li, H.Vallese, F.Clarke, O.B.

(2026) Sci Adv 12: eadz6794-eadz6794

  • DOI: https://doi.org/10.1126/sciadv.adz6794
  • Primary Citation Related Structures: 
    9Z4W, 9Z5N

  • PubMed Abstract: 

    Vaults are some of the largest ribonucleoprotein complexes known and are highly conserved across eukaryotes, but both their function and key details of their architecture remain unclear. While high-resolution structures of the vault shell are available, the architecture and symmetry of the cap have remained unresolved. Here, we present a 2.25-angstrom cryo-electron microscopy structure of the vault cap, revealing an unexpected 13-fold symmetric arrangement that contrasts with the 39-fold symmetry of the vault body, with each repeating module of the cap formed by an asymmetric homotrimer of adjacent subunits. The center of the cap features an unusual architecture, consisting of two concentric β barrels surrounded by an interwoven two-layer stack of α helices. The vault cap features a positively charged exterior and a negatively charged interior surface, with implications for binding partner recruitment and engineering of modified vault particles.


  • Organizational Affiliation
    • Department of Anesthesiology, Columbia University Irving Medical Center, New York, NY 10032, USA.

Macromolecule Content 

  • Total Structure Weight: 577.16 kDa 
  • Atom Count: 27,703 
  • Modeled Residue Count: 3,653 
  • Deposited Residue Count: 5,460 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Major vault protein140Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SVM1 (Oryctolagus cuniculus)
Explore G1SVM1 
Go to UniProtKB:  G1SVM1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1SVM1
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.25 Å
  • Aggregation State: TISSUE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2026-01-21
    Type: Initial release
  • Version 1.1: 2026-08-05
    Changes: Data collection, Database references