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- PDB-9bw5: Human Vault Cage -

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Basic information

Entry
Database: PDB / ID: 9bw5
TitleHuman Vault Cage
ComponentsMajor vault protein
KeywordsPROTEIN TRANSPORT / Vault / Vault Cage / MVP / Major Vault Protein / SPFH / PARP4 / Poly(ADP-ribose)Polymerase 4 / Poly(ADP-ribose)Polymerase / MINT / Ribonucleoprotein / Megadalton complex / TEP1 / vault RNA
Function / homology
Function and homology information


negative regulation of protein tyrosine kinase activity / protein activation cascade / negative regulation of protein autophosphorylation / ERBB signaling pathway / negative regulation of epidermal growth factor receptor signaling pathway / mRNA transport / nuclear pore / protein transport / protein phosphatase binding / secretory granule lumen ...negative regulation of protein tyrosine kinase activity / protein activation cascade / negative regulation of protein autophosphorylation / ERBB signaling pathway / negative regulation of epidermal growth factor receptor signaling pathway / mRNA transport / nuclear pore / protein transport / protein phosphatase binding / secretory granule lumen / ficolin-1-rich granule lumen / cytoskeleton / cell population proliferation / ribonucleoprotein complex / Neutrophil degranulation / protein kinase binding / perinuclear region of cytoplasm / extracellular exosome / extracellular region / identical protein binding / nucleus / membrane / cytosol / cytoplasm
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: 3.3 Å
AuthorsLodwick, J.E. / Zhao, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM143052 United States
Citation
Journal: bioRxiv / Year: 2024
Title: Structural Insights into the Roles of PARP4 and NAD in the Human Vault Cage.
Abstract: Vault is a massive ribonucleoprotein complex found across Eukaryota. The major vault protein (MVP) oligomerizes into an ovular cage, which contains several minor vault components (MVCs) and is ...Vault is a massive ribonucleoprotein complex found across Eukaryota. The major vault protein (MVP) oligomerizes into an ovular cage, which contains several minor vault components (MVCs) and is thought to transport transiently bound "cargo" molecules. Vertebrate vaults house a poly (ADP-ribose) polymerase (known as PARP4 in humans), which is the only MVC with known enzymatic activity. Despite being discovered decades ago, the molecular basis for PARP4's interaction with MVP remains unclear. In this study, we determined the structure of the human vault cage in complex with PARP4 and its enzymatic substrate NAD . The structures reveal atomic-level details of the protein-binding interface, as well as unexpected NAD -binding pockets within the interior of the vault cage. In addition, proteomics data show that human vaults purified from wild-type and PARP4-depleted cells interact with distinct subsets of proteins. Our results thereby support a model in which PARP4's specific incorporation into the vault cage helps to regulate vault's selection of cargo and its subcellular localization. Further, PARP4's proximity to MVP's NAD -binding sites could support its enzymatic function within the vault.
#1: Journal: Protein Sci / Year: 2018
Title: UCSF ChimeraX: Meeting modern challenges in visualization and analysis.
Authors: Thomas D Goddard / Conrad C Huang / Elaine C Meng / Eric F Pettersen / Gregory S Couch / John H Morris / Thomas E Ferrin /
Abstract: UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and ...UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and disparate types of data attendant with cutting-edge experimental methods, while providing advanced options for high-quality rendering (interactive ambient occlusion, reliable molecular surface calculations, etc.) and professional approaches to software design and distribution. This article highlights some specific advances in the areas of visualization and usability, performance, and extensibility. ChimeraX is free for noncommercial use and is available from http://www.rbvi.ucsf.edu/chimerax/ for Windows, Mac, and Linux.
#2: Journal: Science / Year: 2009
Title: The structure of rat liver vault at 3.5 angstrom resolution.
Authors: Hideaki Tanaka / Koji Kato / Eiki Yamashita / Tomoyuki Sumizawa / Yong Zhou / Min Yao / Kenji Iwasaki / Masato Yoshimura / Tomitake Tsukihara /
Abstract: Vaults are among the largest cytoplasmic ribonucleoprotein particles and are found in numerous eukaryotic species. Roles in multidrug resistance and innate immunity have been suggested, but the ...Vaults are among the largest cytoplasmic ribonucleoprotein particles and are found in numerous eukaryotic species. Roles in multidrug resistance and innate immunity have been suggested, but the cellular function remains unclear. We have determined the x-ray structure of rat liver vault at 3.5 angstrom resolution and show that the cage structure consists of a dimer of half-vaults, with each half-vault comprising 39 identical major vault protein (MVP) chains. Each MVP monomer folds into 12 domains: nine structural repeat domains, a shoulder domain, a cap-helix domain, and a cap-ring domain. Interactions between the 42-turn-long cap-helix domains are key to stabilizing the particle. The shoulder domain is structurally similar to a core domain of stomatin, a lipid-raft component in erythrocytes and epithelial cells.
History
DepositionMay 20, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2025Provider: 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


Theoretical massNumber of molelcules
Total (without water)198,9062
Polymers198,9062
Non-polymers00
Water00
1
A: Major vault protein
B: Major vault protein
x 39


Theoretical massNumber of molelcules
Total (without water)7,757,31678
Polymers7,757,31678
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation38

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Components

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


Mass: 99452.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MVP, LRP / Production host: Trichoplusia ni (cabbage looper) / 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: Oligomerized human MVP / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 7.8 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 8 / Details: 50 mM HEPES, 5 mM MgCl2, 5 mM CaCl2, 0.25 mM DTT
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMHEPESC8H18N2O4S1
25 mMMagnesium chlorideMgCl21
35 mMCalcium chlorideCaCl21
40.25 mMDTTC4H10O2S21
SpecimenConc.: 1.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Sample was monodisperse
Specimen supportDetails: Quantifoil grids with a 2 nm continuous carbon coating were subjected to a 15 s, 5W plasma cleaning program in O2 gas
Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K
Details: Vitrification carried out under standard conditions

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Details: Preliminary grid screening was performed manually.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 64000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 45 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6968
Details: Images were collected in movie mode, with 40 frames per image.
EM imaging opticsEnergyfilter name: GIF Bioquantum

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC3.3.1particle selectionManual templates were generated for the first round of picking
2EPUimage acquisition
4cryoSPARC3.3.1CTF correction
7Coot0.8.9.2model fitting
9PHENIX1.12model refinement
10cryoSPARC3.3.1initial Euler assignment
11cryoSPARC3.3.1final Euler assignment
12cryoSPARC3.3.1classification
13cryoSPARC3.3.13D reconstructioncryoSPARC Homogeneous Refinement was performed. The program was instructed to optimize the per-particle defocus and per-exposure-group CTF parameters, fit the anisotropic beam magnification, and apply Ewald sphere correction using the correct curvature sign.
CTF correctionDetails: CTF correction was performed when movies were imported into cryoSPARC Live
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 205194
SymmetryPoint symmetry: D39 (2x39 fold dihedral)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 98674 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Details: The starting model was the rat homologue of MVP from a previous crystal structure of the vault cage (PDB accession no 4V60). The final model was refined in real space and validated using PHENIX.
Atomic model buildingPDB-ID: 4v60

4v60


Pdb chain-ID: A / Accession code: 4v60 / Chain residue range: 1-845 / Pdb chain residue range: 1-845 / Source name: PDB / Type: experimental model

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