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Yorodumi- PDB-1vyi: Structure of the c-terminal domain of the polymerase cofactor of ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vyi | ||||||
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Title | Structure of the c-terminal domain of the polymerase cofactor of rabies virus: insights in function and evolution. | ||||||
Components | RNA POLYMERASE ALPHA SUBUNIT | ||||||
Keywords | TRANSFERASE / RABIES VIRUS / REPLICATION / TRANSCRIPTION / POLYMERASE / RNA-DIRECTED RNA POLYMERASE / PHOSPHORYLATION | ||||||
Function / homology | Function and homology information virion component => GO:0044423 / microtubule-dependent intracellular transport of viral material towards nucleus / viral transcription / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / host cell cytoplasm / symbiont entry into host cell / RNA-dependent RNA polymerase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus Similarity search - Function | ||||||
Biological species | Rabies virus CVS-11 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å | ||||||
Authors | Mavrakis, M. / McCarthy, A.A. / Roche, S. / Blondel, D. / Ruigrok, R.W.H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: Structure and Function of the C-Terminal Domain of the Polymerase Cofactor of Rabies Virus Authors: Mavrakis, M. / Mccarthy, A.A. / Roche, S. / Blondel, D. / Ruigrok, R.W.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vyi.cif.gz | 35.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vyi.ent.gz | 27.1 KB | Display | PDB format |
PDBx/mmJSON format | 1vyi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vy/1vyi ftp://data.pdbj.org/pub/pdb/validation_reports/vy/1vyi | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 12712.466 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN, RESIDUES 186-297 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rabies virus CVS-11 / Plasmid: ACNPVM1 / Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P22363, RNA-directed RNA polymerase | ||||
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#2: Chemical | ChemComp-GOL / #3: Water | ChemComp-HOH / | Compound details | THIS PROTEIN IS PROBABLY A COMPONENT OF THE ACTIVE POLYMERASE AND MAY FUNCTION IN TEMPLATE BINDING. ...THIS PROTEIN IS PROBABLY A COMPONENT OF THE ACTIVE POLYMERASE | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 47.7 % |
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Crystal grow | pH: 5.5 Details: 0.2M (NH4)2SO4 0.1M BIS-TRIS, PH=5.5, 25% (W/V) PEG3350, pH 5.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 11, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→30 Å / Num. obs: 19783 / % possible obs: 98.5 % / Redundancy: 6 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 1.5→1.6 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 7.1 / % possible all: 93.6 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.5→30 Å / SU B: 1.045 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.07
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Displacement parameters | Biso mean: 19.892 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→30 Å
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