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- EMDB-53423: Human vault protein - committed conformation -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-53423
TitleHuman vault protein - committed conformation
Map datahuman vault protein - committed conformation
Sample
  • Complex: Vault protein
    • Protein or peptide: Major vault protein
KeywordsVault protein / vault / MVP / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


protein activation cascade / ERBB signaling pathway / negative regulation of epidermal growth factor receptor signaling pathway / mRNA transport / nuclear pore / protein transport / secretory granule lumen / protein phosphatase binding / ficolin-1-rich granule lumen / cytoskeleton ...protein activation cascade / ERBB signaling pathway / negative regulation of epidermal growth factor receptor signaling pathway / mRNA transport / nuclear pore / protein transport / secretory granule lumen / protein phosphatase binding / ficolin-1-rich granule lumen / cytoskeleton / cell population proliferation / intracellular signal transduction / ribonucleoprotein complex / Neutrophil degranulation / protein kinase binding / perinuclear region of cytoplasm / extracellular exosome / extracellular region / membrane / identical protein binding / nucleus / cytoplasm / 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 speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.45 Å
AuthorsLapenta F / Marechal N / Durand A / Aupic J / Cassetta A
Funding support Slovenia, 1 items
OrganizationGrant numberCountry
Slovenian Research AgencyZ1-3194 Slovenia
CitationJournal: To Be Published
Title: Structural flexibility of the human vault protein revealed by high-resolution cryo-EM and molecular dynamics simulations
Authors: Lapenta F / Palacio-Rodriguez K / Cruz Leon S / Marrancone S / Aupic J / Marechal N / Durand A / Moussaoui D / Covaceuszach S / Gangupam B / d Ercole C / Parra C / Cotugno D / Tomaino G / ...Authors: Lapenta F / Palacio-Rodriguez K / Cruz Leon S / Marrancone S / Aupic J / Marechal N / Durand A / Moussaoui D / Covaceuszach S / Gangupam B / d Ercole C / Parra C / Cotugno D / Tomaino G / Tortora P / de Marco A / Cassetta A / Magistrato A / Hummer G
History
DepositionApr 15, 2025-
Header (metadata) releaseMay 6, 2026-
Map releaseMay 6, 2026-
UpdateMay 6, 2026-
Current statusMay 6, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53423.png

Downloads & links

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Map

FileDownload / File: emd_53423.map.gz / Format: CCP4 / Size: 4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationhuman vault protein - committed conformation
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 1024 pix.
= 861.798 Å		0.84 Å/pix.
x 1024 pix.
= 861.798 Å		0.84 Å/pix.
x 1024 pix.
= 861.798 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8416 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-0.4177708 - 1.7092019
Average (Standard dev.)0.004476188 (±0.095016025)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions102410241024
Spacing102410241024
CellA=B=C: 861.7984 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53423_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: human vault protein - committed conformation - sharpened map

Fileemd_53423_additional_1.map
Annotationhuman vault protein - committed conformation - sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: human vault protein - committed conformation - half map A

Fileemd_53423_half_map_1.map
Annotationhuman vault protein - committed conformation - half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: human vault protein - committed conformation - half map B

Fileemd_53423_half_map_2.map
Annotationhuman vault protein - committed conformation - half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Vault protein

EntireName: Vault protein
Components
  • Complex: Vault protein
    • Protein or peptide: Major vault protein

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Supramolecule #1: Vault protein

SupramoleculeName: Vault protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: 78-mer MVP assembly
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.66 MDa

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Macromolecule #1: Major vault protein

MacromoleculeName: Major vault protein / type: protein_or_peptide / ID: 1 / Number of copies: 78 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 99.452766 KDa
Recombinant expressionOrganism: Komagataella phaffii (fungus)
SequenceString: MATEEFIIRI PPYHYIHVLD QNSNVSRVEV GPKTYIRQDN ERVLFAPMRM VTVPPRHYCT VANPVSRDAQ GLVLFDVTGQ VRLRHADLE IRLAQDPFPL YPGEVLEKDI TPLQVVLPNT ALHLKALLDF EDKDGDKVVA GDEWLFEGPG TYIPRKEVEV V EIIQATII ...String:
MATEEFIIRI PPYHYIHVLD QNSNVSRVEV GPKTYIRQDN ERVLFAPMRM VTVPPRHYCT VANPVSRDAQ GLVLFDVTGQ VRLRHADLE IRLAQDPFPL YPGEVLEKDI TPLQVVLPNT ALHLKALLDF EDKDGDKVVA GDEWLFEGPG TYIPRKEVEV V EIIQATII RQNQALRLRA RKECWDRDGK ERVTGEEWLV TTVGAYLPAV FEEVLDLVDA VILTEKTALH LRARRNFRDF RG VSRRTGE EWLVTVQDTE AHVPDVHEEV LGVVPITTLG PHNYCVILDP VGPDGKNQLG QKRVVKGEKS FFLQPGEQLE QGI QDVYVL SEQQGLLLRA LQPLEEGEDE EKVSHQAGDH WLIRGPLEYV PSAKVEVVEE RQAIPLDENE GIYVQDVKTG KVRA VIGST YMLTQDEVLW EKELPPGVEE LLNKGQDPLA DRGEKDTAKS LQPLAPRNKT RVVSYRVPHN AAVQVYDYRE KRARV VFGP ELVSLGPEEQ FTVLSLSAGR PKRPHARRAL CLLLGPDFFT DVITIETADH ARLQLQLAYN WHFEVNDRKD PQETAK LFS VPDFVGDACK AIASRVRGAV ASVTFDDFHK NSARIIRTAV FGFETSEAKG PDGMALPRPR DQAVFPQNGL VVSSVDV QS VEPVDQRTRD ALQRSVQLAI EITTNSQEAA AKHEAQRLEQ EARGRLERQK ILDQSEAEKA RKELLELEAL SMAVESTG T AKAEAESRAE AARIEGEGSV LQAKLKAQAL AIETEAELQR VQKVRELELV YARAQLELEV SKAQQLAEVE VKKFKQMTE AIGPSTIRDL AVAGPEMQVK LLQSLGLKST LITDGSTPIN LFNTAFGLLG MGPEGQPLGR RVASGPSPGE GISPQSAQAP QAPGDNHVV PVLR

UniProtKB: Major vault protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.38 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
25.0 mMC8H18N2O4SHEPES
150.0 mMNaClsodium chloride
5.0 mMCaCl2calcium chloride
1.0 mMC9H15O6PTCEP

Details: 25 mM HEPES, 150 mM NaCl, 5 mM CaCl2, 1mM TCEP, pH 7.5
GridModel: Homemade / Material: GOLD / Support film - Material: GOLD / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec.
Details: Gold film grids functionalised with 2D streptavidin crystals
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV
Detailsmonodisperse sample, biotinylated with 10 molar excess of biotinylation reagent (NHS-PEG12-biotin) for 30 minutes at room temperature

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 6895 / Average exposure time: 1.498 sec. / Average electron dose: 50.15 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 2.33 µm / Nominal defocus min: 0.551 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 63814
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4hl8

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.45 Å / Resolution method: FSC 0.143 CUT-OFF / Details: Relaxed D39 symmetry (maximization) / Number images used: 23998
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 4 / Avg.num./class: 8857
FSC plot (resolution estimation)

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