[English] 日本語
Yorodumi
- PDB-7pkz: Vault structure in committed conformation -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7pkz
TitleVault structure in committed conformation
ComponentsMajor vault protein
KeywordsSTRUCTURAL PROTEIN / Transport
Function / homology
Function and homology information


protein activation cascade / ERBB signaling pathway / Neutrophil degranulation / negative regulation of epidermal growth factor receptor signaling pathway / protein phosphatase binding / cytoskeleton / cell population proliferation / ribonucleoprotein complex / protein kinase binding / perinuclear region of cytoplasm ...protein activation cascade / ERBB signaling pathway / Neutrophil degranulation / negative regulation of epidermal growth factor receptor signaling pathway / protein phosphatase binding / cytoskeleton / cell population proliferation / 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: 9.8 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 27, 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

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-13483
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-13483
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)7,481,92178
Polymers7,481,92178
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

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


Mass: 95922.062 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

-
Experimental details

-
Experiment

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

-
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

-
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: 41.9 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

-
Processing

EM software
IDNameCategory
7UCSF Chimeramodel fitting
9PHENIXmodel refinement
12RELIONclassification
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 9.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 20864 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model buildingPDB-ID: 4HL8

4hl8


Accession code: 4HL8 / Source name: PDB / Type: experimental model

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more