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

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Open data


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 / protein phosphatase binding / cytoskeleton / cell population proliferation / 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 / protein phosphatase binding / cytoskeleton / cell population proliferation / 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: To Be Published
Title: The vault particle is enclosed by a C13-symmetric cap with a positively charged exterior
Authors: Huan, L. / Oliver, C.
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

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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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