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Yorodumi- PDB-2tmv: VISUALIZATION OF PROTEIN-NUCLEIC ACID INTERACTIONS IN A VIRUS. RE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2tmv | ||||||
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Title | VISUALIZATION OF PROTEIN-NUCLEIC ACID INTERACTIONS IN A VIRUS. REFINED STRUCTURE OF INTACT TOBACCO MOSAIC VIRUS AT 2.9 ANGSTROMS RESOLUTION BY X-RAY FIBER DIFFRACTION | ||||||
Components |
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Keywords | Virus/RNA / VIRUS / Helical virus / Virus-RNA COMPLEX | ||||||
Function / homology | Function and homology information helical viral capsid / structural molecule activity / identical protein binding Similarity search - Function | ||||||
Biological species | Tobacco mosaic virus | ||||||
Method | FIBER DIFFRACTION / Resolution: 2.9 Å | ||||||
Authors | Stubbs, G. / Pattanayek, R. / Namba, K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1989 Title: Visualization of protein-nucleic acid interactions in a virus. Refined structure of intact tobacco mosaic virus at 2.9 A resolution by X-ray fiber diffraction. Authors: Namba, K. / Pattanayek, R. / Stubbs, G. #1: Journal: Science / Year: 1986 Title: Structure of Tobacco Mosaic Virus at 3.6 Angstroms Resolution. Implications for Assembly Authors: Namba, K. / Stubbs, G. #2: Journal: Biophys.J. / Year: 1986 Title: Application of Restrained Least-Squares Refinement to Fiber Diffraction from Macromolecular Assemblies Authors: Stubbs, G. / Namba, K. / Makowski, L. #3: Journal: Acta Crystallogr.,Sect.A / Year: 1985 Title: Solving the Phase Problem in Fiber Diffraction. Application to Tobacco Mosaic Virus at 3.6 Angstroms Resolution Authors: Namba, K. / Stubbs, G. #4: Journal: J.Mol.Biol. / Year: 1981 Title: Structure of the RNA in Tobacco Mosaic Virus Authors: Stubbs, G. / Stauffacher, C. #5: Journal: Nature / Year: 1977 Title: Structure of RNA and RNA Binding Site in Tobacco Mosaic Virus from 4-Angstroms Map Calculated from X-Ray Fibre Diagrams Authors: Stubbs, G. / Warren, S. / Holmes, K. | ||||||
History |
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Remark 650 | HELIX THE ENDS OF ALPHA HELICES ARE OFTEN DIFFICULT TO DEFINE AND IN SEVERAL CASES INCLUDE ONE TURN ...HELIX THE ENDS OF ALPHA HELICES ARE OFTEN DIFFICULT TO DEFINE AND IN SEVERAL CASES INCLUDE ONE TURN OF 3/10 HELIX. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2tmv.cif.gz | 49.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2tmv.ent.gz | 34.7 KB | Display | PDB format |
PDBx/mmJSON format | 2tmv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2tmv_validation.pdf.gz | 363.5 KB | Display | wwPDB validaton report |
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Full document | 2tmv_full_validation.pdf.gz | 397.3 KB | Display | |
Data in XML | 2tmv_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 2tmv_validation.cif.gz | 13.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tm/2tmv ftp://data.pdbj.org/pub/pdb/validation_reports/tm/2tmv | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Atom site foot note | 1: SEE REMARK 7. | ||||||||
Symmetry | Helical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 49 / Num. of operations: 49 / Rise per n subunits: 69 Å / Rotation per n subunits: 1080 °) | ||||||||
Details | TMV IS A ROD-SHAPED VIRUS 3000 ANGSTROMS LONG AND 180 ANGSTROMS IN DIAMETER, WITH A CENTRAL HOLE OF DIAMETER 40 ANGSTROMS. APPROXIMATELY 2130 IDENTICAL PROTEIN SUBUNITS OF MOLECULAR WEIGHT 17500 FORM A RIGHT-HANDED HELIX OF PITCH 23 ANGSTROMS AND LENGTH 69 ANGTROMS WITH 49 SUBUNITS IN THREE TURNS. A SINGLE STRAND OF RNA FOLLOWS THE BASIC HELIX BETWEEN THE PROTEIN SUBUNITS AT A DISTANCE OF 40 ANGSTROMS. THERE ARE THREE NUCLEOTIDES BOUND TO EACH PROTEIN SUBUNIT. |
-Components
#1: RNA chain | Mass: 958.660 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
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#2: Protein | Mass: 17505.426 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tobacco mosaic virus / Strain: vulgare / References: UniProt: P03570, UniProt: P69687*PLUS | ||
#3: Chemical | ChemComp-CA / | ||
#4: Water | ChemComp-HOH / | ||
Nonpolymer details | WATER MOLECULE 45 OCCUPIES A SITE BELIEVED TO BIND CALCIUM AT HIGHER CALCIUM CONCENTRATSequence details | GENERATION OF DIFFERENT SUBUNITS IS MOST EASILY DONE IN POLAR COORDINATES. ASSUME THAT THE ...GENERATION | |
-Experimental details
-Experiment
Experiment | Method: FIBER DIFFRACTION |
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-Sample preparation
Crystal grow | *PLUS Method: unknown |
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-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Rfactor obs: 0.096 / Highest resolution: 2.9 Å Details: THE STRUCTURE WAS DETERMINED BY FIBER DIFFRACTION USING MULTI-DIMENSIONAL ISOMORPHOUS REPLACEMENT WITH LAYER-LINE SPLITTING, SOLVENT FLATTENING REFINEMENT AND RESTRAINED LEAST SQUARES ...Details: THE STRUCTURE WAS DETERMINED BY FIBER DIFFRACTION USING MULTI-DIMENSIONAL ISOMORPHOUS REPLACEMENT WITH LAYER-LINE SPLITTING, SOLVENT FLATTENING REFINEMENT AND RESTRAINED LEAST SQUARES COORDINATE REFINEMENT. THE STRUCTURE INCLUDES 154 OF THE 158 AMINO ACIDS AND THREE RNA NUCLEOTIDES MODELLED AS GAA BUT REPRESENTING THE ENTIRE NUCLEIC ACID CONTENT. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.9 Å
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Refine LS restraints |
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