[English] 日本語
Yorodumi
- PDB-2qzv: Draft Crystal Structure of the Vault Shell at 9 Angstroms Resolution -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2qzv
TitleDraft Crystal Structure of the Vault Shell at 9 Angstroms Resolution
ComponentsMajor vault protein
KeywordsSTRUCTURAL PROTEIN / NANOCAPSULE / BARREL SELF-ASSEMBLED FROM 96 STAVES / MAJOR VAULT PROTEIN / Cytoplasm / Ribonucleoprotein / innate immunity
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 9 Å
AuthorsAnderson, D.H. / Kickhoefer, V.A. / Sievers, S.A. / Rome, L.H. / Eisenberg, D.
Citation
Journal: Plos Biol. / Year: 2007
Title: Draft crystal structure of the vault shell at 9-A resolution.
Authors: Anderson, D.H. / Kickhoefer, V.A. / Sievers, S.A. / Rome, L.H. / Eisenberg, D.
#1: Journal: J.Mol.Biol. / Year: 2004
Title: Cryoelectron Microscopy Imaging of Recombinant and Tissue Derived Vaults: Localization of the Mvp N Termini and Vparp
Authors: Mikyas, Y. / Makabi, M. / Raval-Fernandes, S. / Harrington, L. / Kickhoefer, V.A. / Rome, L.H. / Stewart, P.L.
#2: Journal: J.Mol.Biol. / Year: 2006
Title: Solution structure of a two-repeat fragment of major vault protein
Authors: Kozlov, G. / Vavelyuk, O. / Minailiuc, O. / Banville, D. / Gehring, K. / Ekiel, I.
History
DepositionAug 17, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_ref_seq_dif.details
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 999SEQUENCE THE COMPLETE SEQUENCE OF THE PROTEIN IS "MATEEAIIRIPPYHY ...SEQUENCE THE COMPLETE SEQUENCE OF THE PROTEIN IS "MATEEAIIRIPPYHY IHVLDQNSNVSRVEVGPKTYIRQDNERVLFAPVRMVTVPPRHYCIVANPVSRDTQSS VLFDITGQVRLRHADQEIRLAQDPFPLYPGEVLEKDITPLQVVLPNTALHLKALLDF EDKNGDKVMAGDEWLFEGPGTYIPQKEVEVVEIIQATVIKQNQALRLRARKECFDRE GKGRVTGEEWLVRSVGAYLPAVFEEVLDLVDAVILTEKTALHLRALQNFRDLRGVLH RTGEEWLVTVQDTEAHVPDVYEEVLGVVPITTLGPRHYCVILDPMGPDGKNQLGQKR VVKGEKSFFLQPGERLERGIQDVYVLSEQQGLLLKALQPLEEGESEEKVSHQAGDCW LIRGPLEYVPSAKVEVVEERQAIPLDQNEGIYVQDVKTGKVRAVIGSTYMLTQDEVL WEKELPSGVEELLNLGHDPLADRGQKGTAKPLQPSAPRNKTRVVSYRVPHNAAVQVY DYRAKRARVVFGPELVTLDPEEQFTVLSLSAGRPKRPHARRALCLLLGPDFFTDVIT IETADHARLQLQLAYNWHFELKNRNDPAEAAKLFSVPDFVGDACKAIASRVRGAVAS VTFDDFHKNSARIIRMAVFGFEMSEDTGPDGTLLPKARDQAVFPQNGLVVSSVDVQS VEPVDQRTRDALQRSVQLAIEITTNSQEAAAKHEAQRLEQEARGRLERQKILDQSEA EKARKELLELEAMSMAVESTGNAKAEAESRAEAARIEGEGSVLQAKLKAQALAIETE AELERVKKVREMELIYARAQLELEVSKAQQLANVEAKKFKEMTEALGPGTIRDLAVA GPEMQVKLLQSLGLKSTLITDGSSPINLFSTAFGLLGLGSDGQPPAQK". AT THE N-TERMINUS, AN INSERT MAGCGCPCGCGA IS ALSO PRESENT. IN THIS ENTRY, MODEL RESIDUES OF THE INSERT ARE NUMBERED 3T THROUGH 12T. THE AMINOACID SEQUENCE DATABASE REFERENCE OF THE PROTEIN IS UNP Q62667.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Major vault protein
B: Major vault protein


Theoretical massNumber of molelcules
Total (without water)193,8632
Polymers193,8632
Non-polymers00
Water00
1
A: Major vault protein
B: Major vault protein
x 48


Theoretical massNumber of molelcules
Total (without water)9,305,41096
Polymers9,305,41096
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation47
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
4
A: Major vault protein
B: Major vault protein
x 24


  • crystal asymmetric unit, crystal frame
  • 4.65 MDa, 48 polymers
Theoretical massNumber of molelcules
Total (without water)4,652,70548
Polymers4,652,70548
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation23
Unit cell
Length a, b, c (Å)631.449, 464.724, 584.572
Angle α, β, γ (deg.)90.00, 123.84, 90.00
Int Tables number5
Space group name H-MC121
SymmetryPoint symmetry: (Schoenflies symbol: D24 (2x24 fold dihedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.96783712, 0.25145542, -0.00784046), (-0.25145542, 0.96592583, -0.0612982), (-0.00784046, 0.0612982, 0.9980887)
3generate(0.87354034, 0.48577457, -0.03082753), (-0.48577457, 0.8660254, -0.11841902), (-0.03082753, 0.11841902, 0.99248506)
4generate(0.72353582, 0.68698899, -0.06739467), (-0.68698899, 0.70710678, -0.16746979), (-0.06739467, 0.16746978, 0.98357096)
5generate(0.52804613, 0.84138624, -0.1150499), (-0.84138624, 0.5, -0.20510776), (-0.1150499, 0.20510776, 0.97195387)
6generate(0.30039356, 0.93844441, -0.17054559), (-0.93844442, 0.25881905, -0.22876798), (-0.17054559, 0.22876798, 0.95842549)
7generate(0.05609226, 0.97154914, -0.2300998), (-0.97154915, -0.23683804), (-0.2300998, 0.23683804, 0.94390774)
8generate(-0.18820904, 0.93844441, -0.28965401), (-0.93844442, -0.25881904, -0.22876798), (-0.28965401, 0.22876798, 0.92939)
9generate(-0.41586161, 0.84138624, -0.3451497), (-0.84138624, -0.5, -0.20510776), (-0.3451497, 0.20510776, 0.91586161)
10generate(-0.61135131, 0.68698899, -0.39280493), (-0.68698899, -0.70710678, -0.16746978), (-0.39280492, 0.16746978, 0.90424453)
11generate(-0.76135583, 0.48577457, -0.42937207), (-0.48577458, -0.8660254, -0.11841902), (-0.42937207, 0.11841902, 0.89533042)
12generate(-0.85565261, 0.25145542, -0.45235913), (-0.25145542, -0.96592583, -0.06129819), (-0.45235913, 0.0612982, 0.88972678)
13generate(-0.88781548, -0.46019959), (-1), (-0.46019959, 0.88781548)
14generate(-0.85565261, -0.25145542, -0.45235913), (0.25145542, -0.96592583, 0.0612982), (-0.45235913, -0.0612982, 0.88972678)
15generate(-0.76135582, -0.48577457, -0.42937207), (0.48577457, -0.8660254, 0.11841903), (-0.42937207, -0.11841902, 0.89533042)
16generate(-0.61135131, -0.68698899, -0.39280492), (0.68698899, -0.70710678, 0.16746979), (-0.39280492, -0.16746978, 0.90424453)
17generate(-0.41586161, -0.84138624, -0.34514969), (0.84138624, -0.5, 0.20510777), (-0.34514969, -0.20510776, 0.91586161)
18generate(-0.18820904, -0.93844441, -0.289654), (0.93844441, -0.25881905, 0.22876799), (-0.28965401, -0.22876798, 0.92939)
19generate(0.05609226, -0.97154914, -0.23009979), (0.97154915, 0.23683805), (-0.2300998, -0.23683804, 0.94390774)
20generate(0.30039356, -0.93844441, -0.17054559), (0.93844441, 0.25881904, 0.22876798), (-0.17054559, -0.22876798, 0.95842549)
21generate(0.52804613, -0.84138624, -0.1150499), (0.84138624, 0.5, 0.20510776), (-0.1150499, -0.20510776, 0.97195387)
22generate(0.72353582, -0.68698899, -0.06739467), (0.68698899, 0.70710678, 0.16746979), (-0.06739467, -0.16746978, 0.98357096)
23generate(0.87354034, -0.48577457, -0.03082753), (0.48577457, 0.8660254, 0.11841902), (-0.03082753, -0.11841902, 0.99248506)
24generate(0.96783712, -0.25145542, -0.00784046), (0.25145542, 0.96592583, 0.0612982), (-0.00784046, -0.0612982, 0.9980887)
DetailsTHIS ENTRY CONTAINS TWO PROTEIN CHAINS, A AND B. CHAIN B RESIDUES 3T-715 WERE ROTATED USING TRANSFORM (ROTATION MATRIX AND TRANSLATION VECTOR): 0.991923 -0.126823 -0.00196588 0.126823 0.991445 0.0308693 -0.00196588 -0.0308693 0.999521 0 0 0 TO GENERATE CHAIN A, AND THEN BOTH CHAINS WERE ASSEMBLED BY EDITING THE NON-EQUIVALENT RESIDUES 716-779 ONTO THE ENDS OF CHAINS A AND B RESIDUES 3T-715. THE COMPLETE BIOLOGICAL UNIT (96-MER) CAN BE GENERATED FROM THIS DIMER OF CHAINS A AND B USING 24-FOLD NON-CRYSTALLOGRAPHIC SYMMETRY MATRICES INCLUDED IN MTRIX RECORDS (MATRICES 1-24) AND 2-FOLD CRYSTALLOGRAPHIC SYMMETRY (-1,0,0 0,1,0 0,0,-1) AROUND Y-AXIS. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE

-
Components

#1: Protein Major vault protein / MVP


Mass: 96931.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Mvp / Plasmid: pFASTBAC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q62667

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 7.5 Å3/Da / Density % sol: 84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.5% PEG 8000, 3% GLYCEROL, 0.05M NA MOPS, 0.04M MGCL2, 0.2% N-OCTYL-BETA-D-GLUCOPYRANOSIDE, INITIALLY SATURATED WITH CYCLOHEXANE, PH 6.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K, PH 6.80

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.08 / Wavelength: 1.08 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 16, 2004 / Details: MIRRORS FOCUSED AT 700 MM
RadiationMonochromator: DOUBLE-CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 9→200 Å / Num. obs: 101681 / % possible obs: 98.1 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rsym value: 0.223 / Net I/σ(I): 6.5
Reflection shellResolution: 9→9.5 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 1.2 / Num. unique all: 13869 / Rsym value: 0.63 / % possible all: 95.5

-
Processing

Software
NameVersionClassification
DMmodel building
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
DMphasing
CNS1.1refinement
RefinementMethod to determine structure: AB INITIO PHASING
Starting model: CRYO EM DENSITY

Resolution: 9→200 Å / σ(F): 0
Details: THIS IS A SEMI-REFINED MODEL OF MAJOR VAULT PROTEIN. MANUAL MOLECULAR REPLACEMENT WAS DONE WITH CRYO-EM PHASING MODEL. PHASES WERE REFINED BY DENSITY MODIFICATION USING DM. RESIDUES 113-276 ...Details: THIS IS A SEMI-REFINED MODEL OF MAJOR VAULT PROTEIN. MANUAL MOLECULAR REPLACEMENT WAS DONE WITH CRYO-EM PHASING MODEL. PHASES WERE REFINED BY DENSITY MODIFICATION USING DM. RESIDUES 113-276 WERE ADAPTED FROM PDB ENTRY 1Y7X. RESIDUES 641-779 WERE INITIALLY BUILT BY FITTING POLY-ALA TO DENSITY. THE REMAINDER OF THE MODEL RESULTED FROM FOLD PREDICTIONS. THE DOMAIN MODELS WERE MANUALLY ADJUSTED. THE ASSEMBLED MODEL WAS ENERGY-MINIMIZED WITH CNS. THE MODEL WAS NOT REFINED WITH A GRADIENT-BASED RECIPROCAL-SPACE REFINEMENT PROGRAM.
RfactorNum. reflection% reflection
Rwork0.615 --
obs-101681 98 %
Refinement stepCycle: LAST / Resolution: 9→200 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7404 0 0 0 7404

+
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