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- PDB-7pky: Half-vault structure -

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Basic information

Entry
Database: PDB / ID: 7pky
TitleHalf-vault structure
ComponentsMajor vault protein
KeywordsSTRUCTURAL PROTEIN / Transport
Function / homology
Function and homology information


protein activation cascade / negative regulation of protein autophosphorylation / ERBB signaling pathway / Neutrophil degranulation / negative regulation of epidermal growth factor receptor signaling pathway / protein phosphatase binding / cell population proliferation / cytoskeleton / ribonucleoprotein complex / protein kinase binding ...protein activation cascade / negative regulation of protein autophosphorylation / ERBB signaling pathway / Neutrophil degranulation / negative regulation of epidermal growth factor receptor signaling pathway / protein phosphatase binding / cell population proliferation / cytoskeleton / ribonucleoprotein complex / protein kinase binding / perinuclear region of cytoplasm / identical protein binding / nucleus / 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 speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.9 Å
AuthorsGuerra, P. / Gonzalez-Alamos, M. / Llauro, A. / Casanas, A. / Querol-Audi, J. / de Pablo, P. / Verdaguer, N.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish National Research Council20202CEX003 Spain
Spanish Ministry of Science, Innovation, and UniversitiesBIO2017-83906-P Spain
CitationJournal: Sci Adv / Year: 2022
Title: Symmetry disruption commits vault particles to disassembly.
Authors: Pablo Guerra / María González-Alamos / Aida Llauró / Arnau Casañas / Jordi Querol-Audí / Pedro J de Pablo / Núria Verdaguer /
Abstract: Vaults are ubiquitous ribonucleoprotein particles involved in a diversity of cellular processes, with promising applications as nanodevices for delivery of multiple cargos. The vault shell is ...Vaults are ubiquitous ribonucleoprotein particles involved in a diversity of cellular processes, with promising applications as nanodevices for delivery of multiple cargos. The vault shell is assembled by the symmetrical association of multiple copies of the major vault protein that, initially, generates half vaults. The pairwise, anti-parallel association of two half vaults produces whole vaults. Here, using a combination of vault recombinant reconstitution and structural techniques, we characterized the molecular determinants for the vault opening process. This process commences with a relaxation of the vault waist, causing the expansion of the inner cavity. Then, local disengagement of amino-terminal domains at the vault midsection seeds a conformational change that leads to the aperture, facilitating access to the inner cavity where cargo is hosted. These results inform a hitherto uncharacterized step of the vault cycle and will aid current engineering efforts leveraging vault for tailored cargo delivery.
History
DepositionAug 27, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_initial_refinement_model
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

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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
C: Major vault protein
D: Major vault protein
E: Major vault protein
F: Major vault protein
G: Major vault protein
H: Major vault protein
I: Major vault protein
J: Major vault protein
K: Major vault protein
L: Major vault protein
M: Major vault protein
N: Major vault protein
O: Major vault protein
P: Major vault protein
Q: Major vault protein
R: Major vault protein
S: Major vault protein
T: Major vault protein
U: Major vault protein
V: Major vault protein
W: Major vault protein
X: Major vault protein
Y: Major vault protein
Z: Major vault protein
a: Major vault protein
b: Major vault protein
c: Major vault protein
d: Major vault protein
e: Major vault protein
f: Major vault protein
g: Major vault protein
h: Major vault protein
i: Major vault protein
j: Major vault protein
k: Major vault protein
l: Major vault protein
m: Major vault protein


Theoretical massNumber of molelcules
Total (without water)3,740,88439
Polymers3,740,88439
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "F"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "D"
d_5ens_1chain "E"
d_6ens_1chain "A"
d_7ens_1chain "G"
d_8ens_1chain "H"
d_9ens_1chain "I"
d_10ens_1chain "J"
d_11ens_1chain "K"
d_12ens_1chain "L"
d_13ens_1chain "M"
d_14ens_1chain "N"
d_15ens_1chain "O"
d_16ens_1chain "P"
d_17ens_1chain "Q"
d_18ens_1chain "R"
d_19ens_1chain "S"
d_20ens_1chain "T"
d_21ens_1chain "U"
d_22ens_1chain "V"
d_23ens_1chain "W"
d_24ens_1chain "X"
d_25ens_1chain "Y"
d_26ens_1chain "Z"
d_27ens_1chain "a"
d_28ens_1chain "b"
d_29ens_1chain "c"
d_30ens_1chain "d"
d_31ens_1chain "e"
d_32ens_1chain "f"
d_33ens_1chain "g"
d_34ens_1chain "h"
d_35ens_1chain "i"
d_36ens_1chain "j"
d_37ens_1chain "k"
d_38ens_1chain "l"
d_39ens_1chain "m"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLUPROF1 - 782
d_21ens_1GLUPROB1 - 782
d_31ens_1GLUPROC1 - 782
d_41ens_1GLUPROD1 - 782
d_51ens_1GLUPROE1 - 782
d_61ens_1GLUPROA1 - 782
d_71ens_1GLUPROG1 - 782
d_81ens_1GLUPROH1 - 782
d_91ens_1GLUPROI1 - 782
d_101ens_1GLUPROJ1 - 782
d_111ens_1GLUPROK1 - 782
d_121ens_1GLUPROL1 - 782
d_131ens_1GLUPROM1 - 782
d_141ens_1GLUPRON1 - 782
d_151ens_1GLUPROO1 - 782
d_161ens_1GLUPROP1 - 782
d_171ens_1GLUPROQ1 - 782
d_181ens_1GLUPROR1 - 782
d_191ens_1GLUPROS1 - 782
d_201ens_1GLUPROT1 - 782
d_211ens_1GLUPROU1 - 782
d_221ens_1GLUPROV1 - 782
d_231ens_1GLUPROW1 - 782
d_241ens_1GLUPROX1 - 782
d_251ens_1GLUPROY1 - 782
d_261ens_1GLUPROZ1 - 782
d_271ens_1GLUPROAA1 - 782
d_281ens_1GLUPROBA1 - 782
d_291ens_1GLUPROCA1 - 782
d_301ens_1GLUPRODA1 - 782
d_311ens_1GLUPROEA1 - 782
d_321ens_1GLUPROFA1 - 782
d_331ens_1GLUPROGA1 - 782
d_341ens_1GLUPROHA1 - 782
d_351ens_1GLUPROIA1 - 782
d_361ens_1GLUPROJA1 - 782
d_371ens_1GLUPROKA1 - 782
d_381ens_1GLUPROLA1 - 782
d_391ens_1GLUPROMA1 - 782

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Components

#1: Protein ...
Major vault protein / MVP


Mass: 95920.109 Da / Num. of mol.: 39
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Mvp / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q62667

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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: major vault protein from Rattus norvegicus / Type: CELL / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Rattus norvegicus (Norway rat)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTris buffer pH 7.5Tris1
275 mMSodium ChlorideNaCl1
31 mMMagnesium ChlorideMgCl21
41 mMdithiothreitolDTT1
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 30 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.19.1_4122refinement
PHENIX1.19.1_4122refinement
EM software
IDNameCategory
7UCSF Chimeramodel fitting
9PHENIXmodel refinement
12RELIONclassification
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 7.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 7539 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model buildingPDB-ID: 4HL8

4hl8


Accession code: 4HL8 / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 92.39 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0037244218
ELECTRON MICROSCOPYf_angle_d0.8634330876
ELECTRON MICROSCOPYf_chiral_restr0.050837596
ELECTRON MICROSCOPYf_plane_restr0.006643797
ELECTRON MICROSCOPYf_dihedral_angle_d5.19833345
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2FELECTRON MICROSCOPYNCS constraints0.000713863911009
ens_1d_3FELECTRON MICROSCOPYNCS constraints0.000709961542558
ens_1d_4FELECTRON MICROSCOPYNCS constraints0.000708094320651
ens_1d_5FELECTRON MICROSCOPYNCS constraints0.000714557233523
ens_1d_6FELECTRON MICROSCOPYNCS constraints0.00070693860979
ens_1d_7FELECTRON MICROSCOPYNCS constraints0.000709775856816
ens_1d_8FELECTRON MICROSCOPYNCS constraints0.00070773514025
ens_1d_9FELECTRON MICROSCOPYNCS constraints0.000708147733513
ens_1d_10FELECTRON MICROSCOPYNCS constraints0.000708869755402
ens_1d_11FELECTRON MICROSCOPYNCS constraints0.0405216859115
ens_1d_12FELECTRON MICROSCOPYNCS constraints0.000709814100359
ens_1d_13FELECTRON MICROSCOPYNCS constraints0.0405392553869
ens_1d_14FELECTRON MICROSCOPYNCS constraints0.000711805512955
ens_1d_15FELECTRON MICROSCOPYNCS constraints0.000710806290984
ens_1d_16FELECTRON MICROSCOPYNCS constraints0.000706833404074
ens_1d_17FELECTRON MICROSCOPYNCS constraints0.000705880261944
ens_1d_18FELECTRON MICROSCOPYNCS constraints0.000712963017627
ens_1d_19FELECTRON MICROSCOPYNCS constraints0.000707120710046
ens_1d_20FELECTRON MICROSCOPYNCS constraints0.000708921239937
ens_1d_21FELECTRON MICROSCOPYNCS constraints0.000707274535387
ens_1d_22FELECTRON MICROSCOPYNCS constraints0.000707518753017
ens_1d_23FELECTRON MICROSCOPYNCS constraints0.0405199491597
ens_1d_24FELECTRON MICROSCOPYNCS constraints0.000708181403946
ens_1d_25FELECTRON MICROSCOPYNCS constraints0.000708714306013
ens_1d_26FELECTRON MICROSCOPYNCS constraints0.000707721652685
ens_1d_27FELECTRON MICROSCOPYNCS constraints0.000707413643642
ens_1d_28FELECTRON MICROSCOPYNCS constraints0.000707149978683
ens_1d_29FELECTRON MICROSCOPYNCS constraints0.000708213725639
ens_1d_30FELECTRON MICROSCOPYNCS constraints0.0405370851407
ens_1d_31FELECTRON MICROSCOPYNCS constraints0.0405153434229
ens_1d_32FELECTRON MICROSCOPYNCS constraints0.000710180822155
ens_1d_33FELECTRON MICROSCOPYNCS constraints0.000706086214604
ens_1d_34FELECTRON MICROSCOPYNCS constraints0.000708087875332
ens_1d_35FELECTRON MICROSCOPYNCS constraints0.000711493917566
ens_1d_36FELECTRON MICROSCOPYNCS constraints0.000703626461372
ens_1d_37FELECTRON MICROSCOPYNCS constraints0.000711723639311
ens_1d_38FELECTRON MICROSCOPYNCS constraints0.000706658805041
ens_1d_39FELECTRON MICROSCOPYNCS constraints0.000711614176261

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