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- PDB-9z4w: Cryo-EM structure of rabbit major vault protein complex -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 9z4w
TitleCryo-EM structure of rabbit major vault protein complex
ComponentsMajor vault protein
KeywordsSTRUCTURAL PROTEIN / complex / MVP / vault cap / trafficking
Function / homology
Function and homology information


protein activation cascade / ERBB signaling pathway / negative regulation of epidermal growth factor receptor signaling pathway / cell population proliferation / protein phosphatase binding / cytoskeleton / ribonucleoprotein complex / protein kinase binding / perinuclear region of cytoplasm / identical protein binding ...protein activation cascade / ERBB signaling pathway / negative regulation of epidermal growth factor receptor signaling pathway / cell population proliferation / protein phosphatase binding / cytoskeleton / ribonucleoprotein complex / protein kinase binding / perinuclear region of cytoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
Major vault protein, N-terminal / Major vault protein, shoulder domain / Major vault protein / Major vault protein repeat domain 3 / Major vault protein repeat domain 2 / Major vault protein repeat domain 4 / Major vault protein repeat domain / Major vault protein repeat domain superfamily / Major vault protein repeat domain 2 superfamily / Major Vault Protein repeat domain ...Major vault protein, N-terminal / Major vault protein, shoulder domain / Major vault protein / Major vault protein repeat domain 3 / Major vault protein repeat domain 2 / Major vault protein repeat domain 4 / Major vault protein repeat domain / Major vault protein repeat domain superfamily / Major vault protein repeat domain 2 superfamily / Major Vault Protein repeat domain / Shoulder domain / Major Vault Protein repeat domain / Major Vault Protein Repeat domain / Major Vault Protein repeat domain / MVP (vault) repeat profile. / Band 7/SPFH domain superfamily
Similarity search - Domain/homology
Biological speciesOryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsLi, H. / Clarke, O.B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Adv / Year: 2026
Title: The vault particle is enclosed by a 13-symmetric cap with a positively charged exterior.
Authors: Huan Li / Francesca Vallese / Oliver B Clarke /
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- ...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.
History
DepositionNov 11, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.1Aug 5, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major vault protein
B: Major vault protein
C: Major vault protein
D: Major vault protein
E: Major vault protein
F: Major vault protein
G: Major vault protein
H: Major vault protein
I: Major vault protein
J: Major vault protein
K: Major vault protein
L: Major vault protein
M: Major vault protein
N: Major vault protein
O: Major vault protein
P: Major vault protein
Q: Major vault protein
R: Major vault protein
S: Major vault protein
T: Major vault protein
U: Major vault protein
V: Major vault protein
W: Major vault protein
X: Major vault protein
Y: Major vault protein
Z: Major vault protein
a: Major vault protein
b: Major vault protein
c: Major vault protein
d: Major vault protein
e: Major vault protein
f: Major vault protein
g: Major vault protein
h: Major vault protein
i: Major vault protein
j: Major vault protein
k: Major vault protein
l: Major vault protein
m: Major vault protein
n: Major vault protein
o: Major vault protein
p: Major vault protein
q: Major vault protein
r: Major vault protein
s: Major vault protein
t: Major vault protein
u: Major vault protein
v: Major vault protein
w: Major vault protein
x: Major vault protein
y: Major vault protein
z: Major vault protein
0: Major vault protein
1: Major vault protein
2: Major vault protein
3: Major vault protein
4: Major vault protein
5: Major vault protein
6: Major vault protein
7: Major vault protein
8: Major vault protein
9: Major vault protein
AA: Major vault protein
AB: Major vault protein
AC: Major vault protein
AD: Major vault protein
AE: Major vault protein
AF: Major vault protein
AG: Major vault protein
AH: Major vault protein
AI: Major vault protein
AJ: Major vault protein
AK: Major vault protein
AL: Major vault protein
AM: Major vault protein
AN: Major vault protein
AO: Major vault protein
AP: Major vault protein


Theoretical massNumber of molelcules
Total (without water)7,698,22278
Polymers7,698,22278
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
2given(0.885456, -0.464723), (0.464723, 0.885456), (1)224.03157, -135.4318
3given(0.568065, -0.822984), (0.822984, 0.568065), (1)485.33997, -151.23805
4given(0.120537, -0.992709), (0.992709, 0.120537), (1)724.0626, -43.79772
5given(-0.354605, -0.935016), (0.935016, -0.354605), (1)885.51097, 162.27591
6given(-0.748511, -0.663123), (0.663123, -0.748511), (1)932.69922, 419.77384
7given(-0.970942, -0.239316), (0.239316, -0.970942), (1)854.81708, 669.70641
8given(-0.970942, 0.239316), (-0.239316, -0.970942), (1)669.70641, 854.81708
9given(-0.748511, 0.663123), (-0.663123, -0.748511), (1)419.77384, 932.69922
10given(-0.354605, 0.935016), (-0.935016, -0.354605), (1)162.27591, 885.51097
11given(0.120537, 0.992709), (-0.992709, 0.120537), (1)-43.79772, 724.0626
12given(0.568065, 0.822984), (-0.822984, 0.568065), (1)-151.23805, 485.33997
13given(0.885456, 0.464723), (-0.464723, 0.885456), (1)-135.4318, 224.03157

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Components

#1: Protein ...
Major vault protein


Mass: 98695.156 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SVM1
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: TISSUE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Major vault protein complex / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Buffer solutionpH: 6.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
EM stainingType: NEGATIVE / Material: Uranyl Acetate
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 34.4 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1SerialEMparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 159668 / Symmetry type: POINT

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