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- EMDB-53440: 39-mer half of the human vault protein -

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Basic information

Entry
Database: EMDB / ID: EMD-53440
Title39-mer half of the human vault protein
Map data39-mer half human vault
Sample
  • Complex: half human vault protein
    • Protein or peptide: Major Vault Protein (MVP)
KeywordsVault protein / vault / MVP / TRANSPORT PROTEIN / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


protein activation cascade / ERBB signaling pathway / negative regulation of epidermal growth factor receptor signaling pathway / nuclear pore / mRNA transport / 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 / nuclear pore / mRNA transport / 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: 9.89 Å
AuthorsLapenta F / Marechal N / Durand A / Aupic J / Cassetta A
Funding support Slovenia, 1 items
OrganizationGrant numberCountry
Slovenian Research AgencyZ1-3194 Slovenia
CitationJournal: Nat Commun / Year: 2026
Title: Structural flexibility of the human vault particle revealed by high-resolution cryo-EM and molecular dynamics simulations.
Authors: Fabio Lapenta / Karen Palacio-Rodriguez / Sergio Cruz-León / Simone Marrancone / Jana Aupič / Nils Marechal / Alexandre Durand / Dihia Moussaoui / Sonia Covaceuszach / Bhavani Gangupam / ...Authors: Fabio Lapenta / Karen Palacio-Rodriguez / Sergio Cruz-León / Simone Marrancone / Jana Aupič / Nils Marechal / Alexandre Durand / Dihia Moussaoui / Sonia Covaceuszach / Bhavani Gangupam / Claudia D'Ercole / Cristian Parra / Davide Cotugno / Giulia Tomaino / Paolo Tortora / Ario de Marco / Alberto Cassetta / Alessandra Magistrato / Gerhard Hummer /
Abstract: Vaults are massive ribonucleoprotein complexes, highly conserved and abundant in eukaryotic cells, yet with unclear function. Their thin-walled barrel-shape architecture is composed of two ...Vaults are massive ribonucleoprotein complexes, highly conserved and abundant in eukaryotic cells, yet with unclear function. Their thin-walled barrel-shape architecture is composed of two symmetrical, antiparallel half-shells, each containing 39 copies of the major vault protein (MVP). The spacious lumen of the vault suggests a role in cellular transport. Although vaults are thought to undergo conformational changes to facilitate cargo exchange, the molecular basis for their inherent flexibility remains unknown. Here, we integrate cryogenic electron microscopy (cryo-EM) and multi-scale molecular dynamics (MD) simulations to reveal the structural determinants of the human vault particle's flexibility. Cryo-EM identified two high-resolution alternative conformational states: a symmetric and an asymmetric structure, pointing to the vault shell's structural plasticity. MD simulations of these conformations revealed that these structures are flexible and exhibit breathing-like motions, and porous solvent-exposed surfaces. Mutagenesis disrupting persistent MD-identified inter-half contacts reduced full MVP shell assembly, confirming the functional relevance of these flexibility determinants. Together, these findings establish the molecular basis for the human vault particle's conformational plasticity.
History
DepositionApr 15, 2025-
Header (metadata) releaseApr 29, 2026-
Map releaseApr 29, 2026-
UpdateMay 13, 2026-
Current statusMay 13, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53440.png

Downloads & links

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Map

FileDownload / File: emd_53440.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation39-mer half human vault
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 800 pix.
= 673.28 Å		0.84 Å/pix.
x 800 pix.
= 673.28 Å		0.84 Å/pix.
x 800 pix.
= 673.28 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: 0.3
Minimum - Maximum-0.3217404 - 1.1060369
Average (Standard dev.)0.0065357373 (±0.083615206)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions800800800
Spacing800800800
CellA=B=C: 673.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53440_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: 39-mer half human vault - sharpened

Fileemd_53440_additional_1.map
Annotation39-mer half human vault - sharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: 39-mer half human vault - half map B

Fileemd_53440_half_map_1.map
Annotation39-mer half human vault - half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: 39-mer half human vault - half map A

Fileemd_53440_half_map_2.map
Annotation39-mer half human vault - half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : half human vault protein

EntireName: half human vault protein
Components
  • Complex: half human vault protein
    • Protein or peptide: Major Vault Protein (MVP)

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Supramolecule #1: half human vault protein

SupramoleculeName: half human vault protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: 39-mer MVP assembly
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.66 MDa

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Macromolecule #1: Major Vault Protein (MVP)

MacromoleculeName: Major Vault Protein (MVP) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
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
52.0 mMC8H18N2O4SHEPES
150.0 mMNaClsodium chloride
5.0 mMCaCl2calcium chloride
1.0 mMC9H15O6PTCEO

Details: 25 mM HEPES, 150 mM NaCl, 5 mM CaCl2, 1mM TCEP, pH 7.5
GridModel: Homemade / Support film - Material: GOLD / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec.
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 correctionSoftware - Name: cryoSPARC (ver. 4.5.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4hl8

Final reconstructionResolution.type: BY AUTHOR / Resolution: 9.89 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 3069
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)
Final 3D classificationNumber classes: 4 / Avg.num./class: 8857 / Software - Name: cryoSPARC (ver. 4.5.3)
FSC plot (resolution estimation)

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