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- PDB-9qw9: Human vault protein - primed conformation -

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Basic information

Entry
Database: PDB / ID: 9qw9
TitleHuman vault protein - primed conformation
ComponentsMajor vault protein
KeywordsCYTOSOLIC PROTEIN / Vault protein / vault / MVP / TRANSPORT 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.09 Å
AuthorsLapenta, F. / Marechal, N. / Durand, A. / Aupic, J. / Cassetta, A.
Funding support Slovenia, 1items
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 14, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: FSC / Data content type: FSC / 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
AA: Major vault protein
AB: Major vault protein
AC: Major vault protein
B: Major vault protein
BA: Major vault protein
BB: Major vault protein
C: Major vault protein
CA: Major vault protein
CB: Major vault protein
D: Major vault protein
DA: Major vault protein
DB: Major vault protein
E: Major vault protein
EA: Major vault protein
EB: Major vault protein
F: Major vault protein
FA: Major vault protein
FB: Major vault protein
G: Major vault protein
GA: Major vault protein
GB: Major vault protein
H: Major vault protein
HA: Major vault protein
HB: Major vault protein
I: Major vault protein
IA: Major vault protein
IB: Major vault protein
J: Major vault protein
JA: Major vault protein
JB: Major vault protein
K: Major vault protein
KA: Major vault protein
KB: Major vault protein
L: Major vault protein
LA: Major vault protein
LB: Major vault protein
M: Major vault protein
MA: Major vault protein
MB: Major vault protein
N: Major vault protein
NA: Major vault protein
NB: Major vault protein
O: Major vault protein
OA: Major vault protein
OB: Major vault protein
P: Major vault protein
PA: Major vault protein
PB: Major vault protein
Q: Major vault protein
QA: Major vault protein
QB: Major vault protein
R: Major vault protein
RA: Major vault protein
RB: Major vault protein
S: Major vault protein
SA: Major vault protein
SB: Major vault protein
T: Major vault protein
TA: Major vault protein
TB: Major vault protein
UA: Major vault protein
UB: Major vault protein
V: Major vault protein
VA: Major vault protein
VB: Major vault protein
W: Major vault protein
WA: Major vault protein
WB: Major vault protein
X: Major vault protein
XA: Major vault protein
XB: Major vault protein
Y: Major vault protein
YA: Major vault protein
YB: Major vault protein
Z: Major vault protein
ZA: Major vault protein
ZB: Major vault protein


Theoretical massNumber of molelcules
Total (without water)7,757,31678
Polymers7,757,31678
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ...
Major vault protein / MVP / Lung resistance-related protein


Mass: 99452.766 Da / Num. of mol.: 78
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MVP, LRP / Production host: Komagataella phaffii (fungus) / Strain (production host): SMD1168 / References: UniProt: Q14764
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Vault protein / Type: COMPLEX / Details: 78-mer MVP assembly / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 7.66 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Komagataella phaffii (fungus) / Strain: SMD1168
Buffer solutionpH: 7.5
Details: 25 mM HEPES, 150 mM NaCl, 5 mM CaCl2, 1mM TCEP, pH 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
152 mMHEPESC8H18N2O4S1
2150 mMsodium chlorideNaCl1
35 mMcalcium chlorideCaCl21
41 mMTCEOC9H15O6P1
SpecimenConc.: 0.38 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: monodisperse sample, biotinylated with 10 molar excess of biotinylation reagent (NHS-PEG12-biotin) for 30 minutes at room temperature
Specimen supportDetails: Gold film grids functionalised with 2D streptavidin crystals
Grid material: GOLD / Grid type: Homemade
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen 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: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2330 nm / Nominal defocus min: 551 nm / Cs: 0.01 mm / C2 aperture diameter: 70 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.498 sec. / Electron dose: 50.15 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6895
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.5.3particle selection
2SerialEMimage acquisition
4cryoSPARC4.5.3CTF correction
9cryoSPARC4.5.3initial Euler assignment
10cryoSPARC4.5.3final Euler assignment
11cryoSPARC4.5.3classification
13PHENIX1.21model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 63814
SymmetryPoint symmetry: D39 (2x39 fold dihedral)
3D reconstructionResolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11172 / Num. of class averages: 1 / Symmetry type: POINT

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