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Yorodumi- PDB-2tbv: STRUCTURE OF TOMATO BUSHY STUNT VIRUS. V. COAT PROTEIN SEQUENCE D... -
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-Basic information
Entry | Database: PDB / ID: 2tbv | ||||||
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Title | STRUCTURE OF TOMATO BUSHY STUNT VIRUS. V. COAT PROTEIN SEQUENCE DETERMINATION AND ITS STRUCTURAL IMPLICATIONS | ||||||
Components | TOMATO BUSHY STUNT VIRUS | ||||||
Keywords | VIRUS / Icosahedral virus | ||||||
Function / homology | Function and homology information T=3 icosahedral viral capsid / structural molecule activity / RNA binding Similarity search - Function | ||||||
Biological species | Tomato bushy stunt virus | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.9 Å | ||||||
Authors | Harrison, S.C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1984 Title: Structure of tomato bushy stunt virus. V. Coat protein sequence determination and its structural implications Authors: Hopper, P. / Harrison, S.C. / Sauer, R.T. #1: Journal: J.Mol.Biol. / Year: 1983 Title: Structure of Tomato Bushy Stunt Virus. Iv. The Virus Particle at 2.9 Angstroms Resolution Authors: Olson, A.J. / Bricogne, G. / Harrison, S.C. #2: Journal: J.Mol.Biol. / Year: 1983 Title: Divalent Cation Sites in Tomato Bushy Stunt Virus. Difference Maps at 2.9 Angstroms Resolution Authors: Hogle, J. / Kirchhausen, T. / Harrison, S.C. #3: Journal: Biophys.J. / Year: 1980 Title: Protein Interfaces and Intersubunit Bonding. The Case of Tomato Bushy Stunt Virus Authors: Harrison, S.C. #4: Journal: Nature / Year: 1978 Title: Tomato Bushy Stunt Virus at 2.9 Angstroms Resolution Authors: Harrison, S.C. / Olson, A.J. / Schutt, C.E. / Winkler, F.K. / Bricogne, G. #5: Journal: Nature / Year: 1977 Title: Tomato Bushy Stunt Virus at 5.5-Angstroms Resolution Authors: Winkler, F.K. / Schutt, C.E. / Harrison, S.C. / Bricogne, G. #6: Journal: J.Mol.Biol. / Year: 1969 Title: Structure of Tomato Bushy Stunt Virus. I. The Spherically Averaged Electron Density Authors: Harrison, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2tbv.cif.gz | 166.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2tbv.ent.gz | 124.5 KB | Display | PDB format |
PDBx/mmJSON format | 2tbv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2tbv_validation.pdf.gz | 398.8 KB | Display | wwPDB validaton report |
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Full document | 2tbv_full_validation.pdf.gz | 598.7 KB | Display | |
Data in XML | 2tbv_validation.xml.gz | 50.4 KB | Display | |
Data in CIF | 2tbv_validation.cif.gz | 66.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tb/2tbv ftp://data.pdbj.org/pub/pdb/validation_reports/tb/2tbv | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Atom site foot note | 1: THE CHEMICAL SEQUENCE IN RESIDUES 246 TO 258, 269 TO 275 AND 365 TO 379 COULD NOT BE DETERMINED WELL. RESIDUES AT THESE POSITIONS IN THE COORDINATE LIST WERE BUILT TO FIT THE OBSERVED ELECTRON ...1: THE CHEMICAL SEQUENCE IN RESIDUES 246 TO 258, 269 TO 275 AND 365 TO 379 COULD NOT BE DETERMINED WELL. RESIDUES AT THESE POSITIONS IN THE COORDINATE LIST WERE BUILT TO FIT THE OBSERVED ELECTRON DENSITY. THESE COORDINATES SHOULD BE REGARDED ONLY AS AN APPROXIMATION TO THE CORRECT MODEL IN THIS REGION (SEE REFERENCE 1 ABOVE). 2: RESIDUE 102 IS SER IN THE CHEMICAL SEQUENCE, BUT SHOWS NO SIDE CHAIN DENSITY IN THE MAP. THIS RESIDUE WAS BUILT AS GLY IN THIS MODEL. SIMILARLY, RESIDUE 107 IS GLY IN THE CHEMICAL SEQUENCE, BUT ...2: RESIDUE 102 IS SER IN THE CHEMICAL SEQUENCE, BUT SHOWS NO SIDE CHAIN DENSITY IN THE MAP. THIS RESIDUE WAS BUILT AS GLY IN THIS MODEL. SIMILARLY, RESIDUE 107 IS GLY IN THE CHEMICAL SEQUENCE, BUT APPEARS TO HAVE A SIDE CHAIN IN THE ELECTRON DENSITY. THIS RESIDUE WAS BUILT AS SER. THE DISCREPANCY BETWEEN THE CHEMICAL AND THE CRYSTALLOGRAPHIC DATA IS PRESENTLY UNRESOLVED. 3: THE S (SHELL) AND P (PROJECTION) DOMAINS OF EACH SUBUNIT WERE BUILT SEPARATELY. TO FACILITATE THE MERGING OF THE DOMAINS INTO A SINGLE CONTIGUOUS CHAIN, AN OVERLAP REGION WAS BUILT. THE ATOMS IN ...3: THE S (SHELL) AND P (PROJECTION) DOMAINS OF EACH SUBUNIT WERE BUILT SEPARATELY. TO FACILITATE THE MERGING OF THE DOMAINS INTO A SINGLE CONTIGUOUS CHAIN, AN OVERLAP REGION WAS BUILT. THE ATOMS IN THIS OVERLAP REGION ARE PRESENTED IN THIS ENTRY AS ALTERNATE LOCATIONS *S* AND *P* IN RESIDUES 273, 274 AND 275. 4: CAREFUL MODEL BUILDING AGAINST THE ELECTRON DENSITY INDICATES THAT PRO 290 AND PRO 359 ARE CIS-PROLINES. HOWEVER, THE USUAL CAVEATS APPLIED TO A 2.9 ANGSTROMS STUDY SHOULD BE OBSERVED. 5: SEE REMARK 3. / 6: SEE REMARK 3 AND FTNOTE 1. | ||||||||||||||||||
Symmetry | Point symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral)) | ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 40576.012 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tomato bushy stunt virus / Genus: Tombusvirus / References: UniProt: P11795 #2: Chemical | ChemComp-CA / Compound details | THE S (SHELL) AND P (PROJECTION) DOMAINS OF EACH SUBUNIT WERE BUILT SEPARATELY. TO FACILITATE THE ...THE S (SHELL) AND P (PROJECTION | Sequence details | RESIDUE 102 IS SER IN THE CHEMICAL SEQUENCE, BUT SHOWS NO SIDE CHAIN DENSITY IN THE MAP. THIS ...RESIDUE 102 IS SER IN THE CHEMICAL SEQUENCE, BUT SHOWS NO SIDE CHAIN DENSITY IN THE MAP. THIS RESIDUE WAS BUILT AS GLY IN THIS MODEL. SIMILARLY, RESIDUE 107 IS GLY IN THE CHEMICAL SEQUENCE, BUT APPEARS TO HAVE A SIDE CHAIN IN THE ELECTRON DENSITY. THIS RESIDUE WAS BUILT AS SER. THE DISCREPANC | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal grow | *PLUS Method: otherDetails: Harrison, S.C., (1980) Biophys, J., 32, 139., Harrison, S.C., (1978) Nature, 276, 386., Olson, A.J., (1983) J. Mol. Biol., 171, 61. |
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-Processing
Refinement | Highest resolution: 2.9 Å | ||||||||||||
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Refinement step | Cycle: LAST / Highest resolution: 2.9 Å
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