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- PDB-2qzv: Draft Crystal Structure of the Vault Shell at 9 Angstroms Resolution -
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Open data
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Basic information
Entry | Database: PDB / ID: 2qzv | ||||||
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Title | Draft Crystal Structure of the Vault Shell at 9 Angstroms Resolution | ||||||
![]() | Major vault protein | ||||||
![]() | STRUCTURAL PROTEIN / NANOCAPSULE / BARREL SELF-ASSEMBLED FROM 96 STAVES / MAJOR VAULT PROTEIN / Cytoplasm / Ribonucleoprotein / innate immunity | ||||||
Function / homology | ![]() 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 | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Anderson, D.H. / Kickhoefer, V.A. / Sievers, S.A. / Rome, L.H. / Eisenberg, D. | ||||||
![]() | ![]() 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: ![]() 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 |
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Remark 999 | SEQUENCE 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 viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 224 KB | Display | ![]() |
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PDB format | ![]() | 142.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Symmetry | Point symmetry: (Schoenflies symbol: D24 (2x24 fold dihedral)) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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Details | THIS 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 | Mass: 96931.359 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 7.5 Å3/Da / Density % sol: 84 % |
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Crystal grow | Temperature: 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
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 16, 2004 / Details: MIRRORS FOCUSED AT 700 MM |
Radiation | Monochromator: DOUBLE-CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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
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Refinement | Method 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.
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Refinement step | Cycle: LAST / Resolution: 9→200 Å
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