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- EMDB-73819: Cryo-EM structure of rabbit vault cap -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-73819
TitleCryo-EM structure of rabbit vault cap
Map data
Sample
  • Organelle or cellular component: Major vault protein complex
    • Protein or peptide: Major vault protein
Keywordscomplex / MVP / vault cap / trafficking / STRUCTURAL PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 2.25 Å
AuthorsLi H / Clarke OB
Funding support1 items
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 12, 2025-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73819.png

Downloads & links

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Map

FileDownload / File: emd_73819.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 384 pix.
= 311.04 Å		0.81 Å/pix.
x 384 pix.
= 311.04 Å		0.81 Å/pix.
x 384 pix.
= 311.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.81 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0615
Minimum - Maximum-0.3221451 - 0.5775909
Average (Standard dev.)0.00091888884 (±0.018319294)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 311.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_73819_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_73819_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Major vault protein complex

EntireName: Major vault protein complex
Components
  • Organelle or cellular component: Major vault protein complex
    • Protein or peptide: Major vault protein

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Supramolecule #1: Major vault protein complex

SupramoleculeName: Major vault protein complex / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Oryctolagus cuniculus (rabbit)

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Macromolecule #1: Major vault protein

MacromoleculeName: Major vault protein / type: protein_or_peptide / ID: 1 / Number of copies: 39 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 14.798978 KDa
SequenceString:
LAIETEAELQ RVQKVRELEL VYARAQLELE VSKAQQLAEV EAKKFKQMTE ALGPSTIKDL AVAGPEMQVK LLQSLGLKST LITDGSTPV NLFNTAFGLL GLGADGQPLG RMTAGGPRLQ EAASPQSPSA PLAPGSTHIL P

UniProtKB: Major vault protein

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation statetissue

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Sample preparation

BufferpH: 6.8
StainingType: NEGATIVE / Material: Uranyl Acetate
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 34.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7pkr

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.25 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 129638
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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