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- PDB-7pkr: Vault structure in primmed conformation -

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Basic information

Entry
Database: PDB / ID: 7pkr
TitleVault structure in primmed conformation
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: 3.8 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 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 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

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Structure viewerMolecule:
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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
V: Major vault protein
W: Major vault protein
X: Major vault protein
Y: Major vault protein
Z: Major vault protein
AA: Major vault protein
BA: Major vault protein
CA: Major vault protein
DA: Major vault protein
EA: Major vault protein
FA: Major vault protein
GA: Major vault protein
HA: Major vault protein
IA: Major vault protein
JA: Major vault protein
KA: Major vault protein
LA: Major vault protein
MA: Major vault protein
NA: Major vault protein
OA: Major vault protein
PA: Major vault protein
QA: Major vault protein
RA: Major vault protein
SA: Major vault protein
TA: Major vault protein
UA: Major vault protein
VA: Major vault protein
WA: Major vault protein
XA: Major vault protein
YA: Major vault protein
ZA: Major vault protein
AB: Major vault protein
BB: Major vault protein
CB: Major vault protein
DB: Major vault protein
EB: Major vault protein
FB: Major vault protein
GB: Major vault protein
HB: Major vault protein
IB: Major vault protein
JB: Major vault protein
KB: Major vault protein
LB: Major vault protein
MB: Major vault protein
NB: Major vault protein
OB: Major vault protein
PB: Major vault protein
QB: Major vault protein
RB: Major vault protein
SB: Major vault protein
TB: Major vault protein
UB: Major vault protein
VB: Major vault protein
WB: Major vault protein
XB: Major vault protein
YB: Major vault protein
ZB: Major vault protein
AC: Major vault protein


Theoretical massNumber of molelcules
Total (without water)7,481,76978
Polymers7,481,76978
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "L"
d_2ens_1chain "AA"
d_3ens_1chain "AB"
d_4ens_1chain "AC"
d_5ens_1chain "B"
d_6ens_1chain "BA"
d_7ens_1chain "BB"
d_8ens_1chain "C"
d_9ens_1chain "CA"
d_10ens_1chain "CB"
d_11ens_1chain "D"
d_12ens_1chain "DA"
d_13ens_1chain "DB"
d_14ens_1chain "E"
d_15ens_1chain "EA"
d_16ens_1chain "EB"
d_17ens_1chain "F"
d_18ens_1chain "FA"
d_19ens_1chain "FB"
d_20ens_1chain "G"
d_21ens_1chain "GA"
d_22ens_1chain "GB"
d_23ens_1chain "H"
d_24ens_1chain "HA"
d_25ens_1chain "HB"
d_26ens_1chain "I"
d_27ens_1chain "IA"
d_28ens_1chain "IB"
d_29ens_1chain "J"
d_30ens_1chain "JA"
d_31ens_1chain "JB"
d_32ens_1chain "K"
d_33ens_1chain "KA"
d_34ens_1chain "KB"
d_35ens_1chain "A"
d_36ens_1chain "LA"
d_37ens_1chain "LB"
d_38ens_1chain "M"
d_39ens_1chain "MA"
d_40ens_1chain "MB"
d_41ens_1chain "N"
d_42ens_1chain "NA"
d_43ens_1chain "NB"
d_44ens_1chain "O"
d_45ens_1chain "OA"
d_46ens_1chain "OB"
d_47ens_1chain "P"
d_48ens_1chain "PA"
d_49ens_1chain "PB"
d_50ens_1chain "Q"
d_51ens_1chain "QA"
d_52ens_1chain "QB"
d_53ens_1chain "R"
d_54ens_1chain "RA"
d_55ens_1chain "RB"
d_56ens_1chain "S"
d_57ens_1chain "SA"
d_58ens_1chain "SB"
d_59ens_1chain "T"
d_60ens_1chain "TA"
d_61ens_1chain "TB"
d_62ens_1chain "UA"
d_63ens_1chain "UB"
d_64ens_1chain "V"
d_65ens_1chain "VA"
d_66ens_1chain "VB"
d_67ens_1chain "W"
d_68ens_1chain "WA"
d_69ens_1chain "WB"
d_70ens_1chain "X"
d_71ens_1chain "XA"
d_72ens_1chain "XB"
d_73ens_1chain "Y"
d_74ens_1chain "YA"
d_75ens_1chain "YB"
d_76ens_1chain "Z"
d_77ens_1chain "ZA"
d_78ens_1chain "ZB"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLUPROL1 - 782
d_21ens_1GLUPROL1 - 782
d_31ens_1GLUPROL1 - 782
d_41ens_1GLUPROL1 - 782
d_51ens_1GLUPROL1 - 782
d_61ens_1GLUPROL1 - 782
d_71ens_1GLUPROL1 - 782
d_81ens_1GLUPROL1 - 782
d_91ens_1GLUPROL1 - 782
d_101ens_1GLUPROL1 - 782
d_111ens_1GLUPROL1 - 782
d_121ens_1GLUPROL1 - 782
d_131ens_1GLUPROL1 - 782
d_141ens_1GLUPROL1 - 782
d_151ens_1GLUPROL1 - 782
d_161ens_1GLUPROL1 - 782
d_171ens_1GLUPROL1 - 782
d_181ens_1GLUPROL1 - 782
d_191ens_1GLUPROL1 - 782
d_201ens_1GLUPROL1 - 782
d_211ens_1GLUPROL1 - 782
d_221ens_1GLUPROL1 - 782
d_231ens_1GLUPROL1 - 782
d_241ens_1GLUPROL1 - 782
d_251ens_1GLUPROL1 - 782
d_261ens_1GLUPROL1 - 782
d_271ens_1GLUPROL1 - 782
d_281ens_1GLUPROL1 - 782
d_291ens_1GLUPROL1 - 782
d_301ens_1GLUPROL1 - 782
d_311ens_1GLUPROL1 - 782
d_321ens_1GLUPROL1 - 782
d_331ens_1GLUPROL1 - 782
d_341ens_1GLUPROL1 - 782
d_351ens_1GLUPROL1 - 782
d_361ens_1GLUPROL1 - 782
d_371ens_1GLUPROL1 - 782
d_381ens_1GLUPROL1 - 782
d_391ens_1GLUPROL1 - 782
d_401ens_1GLUPROL1 - 782
d_411ens_1GLUPROL1 - 782
d_421ens_1GLUPROL1 - 782
d_431ens_1GLUPROL1 - 782
d_441ens_1GLUPROL1 - 782
d_451ens_1GLUPROL1 - 782
d_461ens_1GLUPROL1 - 782
d_471ens_1GLUPROL1 - 782
d_481ens_1GLUPROL1 - 782
d_491ens_1GLUPROL1 - 782
d_501ens_1GLUPROL1 - 782
d_511ens_1GLUPROL1 - 782
d_521ens_1GLUPROL1 - 782
d_531ens_1GLUPROL1 - 782
d_541ens_1GLUPROL1 - 782
d_551ens_1GLUPROL1 - 782
d_561ens_1GLUPROL1 - 782
d_571ens_1GLUPROL1 - 782
d_581ens_1GLUPROL1 - 782
d_591ens_1GLUPROL1 - 782
d_601ens_1GLUPROL1 - 782
d_611ens_1GLUPROL1 - 782
d_621ens_1GLUPROL1 - 782
d_631ens_1GLUPROL1 - 782
d_641ens_1GLUPROL1 - 782
d_651ens_1GLUPROL1 - 782
d_661ens_1GLUPROL1 - 782
d_671ens_1GLUPROL1 - 782
d_681ens_1GLUPROL1 - 782
d_691ens_1GLUPROL1 - 782
d_701ens_1GLUPROL1 - 782
d_711ens_1GLUPROL1 - 782
d_721ens_1GLUPROL1 - 782
d_731ens_1GLUPROL1 - 782
d_741ens_1GLUPROL1 - 782
d_751ens_1GLUPROL1 - 782
d_761ens_1GLUPROL1 - 782
d_771ens_1GLUPROL1 - 782
d_781ens_1GLUPROL1 - 782

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Components

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


Mass: 95920.109 Da / Num. of mol.: 78
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
Specimen supportGrid material: GOLD / Grid type: UltrAuFoil R1.2/1.3
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: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9793 / 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: 55.03 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0024487890
ELECTRON MICROSCOPYf_angle_d0.6101661050
ELECTRON MICROSCOPYf_chiral_restr0.042775192
ELECTRON MICROSCOPYf_plane_restr0.004887438
ELECTRON MICROSCOPYf_dihedral_angle_d5.493366690
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2LELECTRON MICROSCOPYNCS constraints0.000707273335537
ens_1d_3LELECTRON MICROSCOPYNCS constraints0.000706090904589
ens_1d_4LELECTRON MICROSCOPYNCS constraints0.0405977792417
ens_1d_5LELECTRON MICROSCOPYNCS constraints0.0405884233373
ens_1d_6LELECTRON MICROSCOPYNCS constraints0.00070809543243
ens_1d_7LELECTRON MICROSCOPYNCS constraints0.000706649056195
ens_1d_8LELECTRON MICROSCOPYNCS constraints0.0405713856615
ens_1d_9LELECTRON MICROSCOPYNCS constraints0.000707701616664
ens_1d_10LELECTRON MICROSCOPYNCS constraints0.000709047801357
ens_1d_11LELECTRON MICROSCOPYNCS constraints0.000706759028481
ens_1d_12LELECTRON MICROSCOPYNCS constraints0.000706342081137
ens_1d_13LELECTRON MICROSCOPYNCS constraints0.000706467570253
ens_1d_14LELECTRON MICROSCOPYNCS constraints0.0573777537688
ens_1d_15LELECTRON MICROSCOPYNCS constraints0.000708338597015
ens_1d_16LELECTRON MICROSCOPYNCS constraints0.040568177975
ens_1d_17LELECTRON MICROSCOPYNCS constraints0.040592080559
ens_1d_18LELECTRON MICROSCOPYNCS constraints0.000705937939092
ens_1d_19LELECTRON MICROSCOPYNCS constraints0.0573784273435
ens_1d_20LELECTRON MICROSCOPYNCS constraints0.0573819507583
ens_1d_21LELECTRON MICROSCOPYNCS constraints0.000703434682111
ens_1d_22LELECTRON MICROSCOPYNCS constraints0.0405891081497
ens_1d_23LELECTRON MICROSCOPYNCS constraints0.0405872603189
ens_1d_24LELECTRON MICROSCOPYNCS constraints0.000705236844329
ens_1d_25LELECTRON MICROSCOPYNCS constraints0.0573833501117
ens_1d_26LELECTRON MICROSCOPYNCS constraints0.0573828896252
ens_1d_27LELECTRON MICROSCOPYNCS constraints0.000706219194436
ens_1d_28LELECTRON MICROSCOPYNCS constraints0.0573781680422
ens_1d_29LELECTRON MICROSCOPYNCS constraints0.000707007200054
ens_1d_30LELECTRON MICROSCOPYNCS constraints0.000708233635795
ens_1d_31LELECTRON MICROSCOPYNCS constraints0.000707247989473
ens_1d_32LELECTRON MICROSCOPYNCS constraints0.0573874449113
ens_1d_33LELECTRON MICROSCOPYNCS constraints0.000705262505177
ens_1d_34LELECTRON MICROSCOPYNCS constraints0.000705962125495
ens_1d_35LELECTRON MICROSCOPYNCS constraints0.0405923382857
ens_1d_36LELECTRON MICROSCOPYNCS constraints0.000704780743614
ens_1d_37LELECTRON MICROSCOPYNCS constraints0.0405889154204
ens_1d_38LELECTRON MICROSCOPYNCS constraints0.0573818845279
ens_1d_39LELECTRON MICROSCOPYNCS constraints0.0405983904418
ens_1d_40LELECTRON MICROSCOPYNCS constraints0.00070905744613
ens_1d_41LELECTRON MICROSCOPYNCS constraints0.0405919912427
ens_1d_42LELECTRON MICROSCOPYNCS constraints0.000707191240798
ens_1d_43LELECTRON MICROSCOPYNCS constraints0.0573786329541
ens_1d_44LELECTRON MICROSCOPYNCS constraints0.0405911046562
ens_1d_45LELECTRON MICROSCOPYNCS constraints0.000706310320235
ens_1d_46LELECTRON MICROSCOPYNCS constraints0.057385598264
ens_1d_47LELECTRON MICROSCOPYNCS constraints0.0405939078449
ens_1d_48LELECTRON MICROSCOPYNCS constraints0.000709757893036
ens_1d_49LELECTRON MICROSCOPYNCS constraints0.0573818089412
ens_1d_50LELECTRON MICROSCOPYNCS constraints0.000706082789163
ens_1d_51LELECTRON MICROSCOPYNCS constraints0.000713642079712
ens_1d_52LELECTRON MICROSCOPYNCS constraints0.0573588762584
ens_1d_53LELECTRON MICROSCOPYNCS constraints0.040588603289
ens_1d_54LELECTRON MICROSCOPYNCS constraints0.000708845343523
ens_1d_55LELECTRON MICROSCOPYNCS constraints0.000708420859622
ens_1d_56LELECTRON MICROSCOPYNCS constraints0.0405891616315
ens_1d_57LELECTRON MICROSCOPYNCS constraints0.000705073824961
ens_1d_58LELECTRON MICROSCOPYNCS constraints0.000703656217809
ens_1d_59LELECTRON MICROSCOPYNCS constraints0.0405964047332
ens_1d_60LELECTRON MICROSCOPYNCS constraints0.00070556371249
ens_1d_61LELECTRON MICROSCOPYNCS constraints0.000703918602073
ens_1d_62LELECTRON MICROSCOPYNCS constraints0.000707193915669
ens_1d_63LELECTRON MICROSCOPYNCS constraints0.0405666267338
ens_1d_64LELECTRON MICROSCOPYNCS constraints0.000704628239949
ens_1d_65LELECTRON MICROSCOPYNCS constraints0.000703128107359
ens_1d_66LELECTRON MICROSCOPYNCS constraints0.0405884418258
ens_1d_67LELECTRON MICROSCOPYNCS constraints0.040588735053
ens_1d_68LELECTRON MICROSCOPYNCS constraints0.000701730268959
ens_1d_69LELECTRON MICROSCOPYNCS constraints0.0573818307791
ens_1d_70LELECTRON MICROSCOPYNCS constraints0.000708552567597
ens_1d_71LELECTRON MICROSCOPYNCS constraints0.000707065410024
ens_1d_72LELECTRON MICROSCOPYNCS constraints0.0405951641051
ens_1d_73LELECTRON MICROSCOPYNCS constraints0.000705889080666
ens_1d_74LELECTRON MICROSCOPYNCS constraints0.000706532749367
ens_1d_75LELECTRON MICROSCOPYNCS constraints0.057384371434
ens_1d_76LELECTRON MICROSCOPYNCS constraints0.00070481864431
ens_1d_77LELECTRON MICROSCOPYNCS constraints0.000704129829174
ens_1d_78LELECTRON MICROSCOPYNCS constraints0.0573803712166

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