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- PDB-2qzv: Draft Crystal Structure of the Vault Shell at 9 Angstroms Resolution -

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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 / 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)
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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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