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- PDB-2r7x: Crystal Structure of Rotavirus SA11 VP1/RNA (UGUGACC)/GTP complex -
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Open data
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Basic information
Entry | Database: PDB / ID: 2r7x | ||||||
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Title | Crystal Structure of Rotavirus SA11 VP1/RNA (UGUGACC)/GTP complex | ||||||
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![]() | transferase/RNA / Viral protein / RNA-dependent RNA polymerase / single subunit polymerase fold / fingers / palm / thumb / right hand configuration / RNA-directed RNA polymerase / transferase-RNA COMPLEX | ||||||
Function / homology | ![]() viral genome replication / virion component / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / nucleotide binding / DNA-templated transcription / RNA binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() ![]() | ||||||
![]() | Lu, X. / Harrison, S.C. / Tao, Y.J. / Patton, J.T. / Nibert, M.L. | ||||||
![]() | ![]() Title: Mechanism for coordinated RNA packaging and genome replication by rotavirus polymerase VP1. Authors: Lu, X. / McDonald, S.M. / Tortorici, M.A. / Tao, Y.J. / Vasquez-Del Carpio, R. / Nibert, M.L. / Patton, J.T. / Harrison, S.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 447.6 KB | Display | ![]() |
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PDB format | ![]() | 359.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1023.6 KB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 82.9 KB | Display | |
Data in CIF | ![]() | 111.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2r7oC ![]() 2r7qSC ![]() 2r7rC ![]() 2r7sC ![]() 2r7tC ![]() 2r7uC ![]() 2r7vC ![]() 2r7wC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Details | there are 2 biological units in the asymmetric unit |
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Components
#1: RNA chain | Mass: 2197.355 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Protein | Mass: 126324.453 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Plasmid details: pCRBac-based transfer vector (invitrogen) is used to produce VP1 gene integrated ACNPV Plasmid: pCRBac / Production host: ![]() ![]() #3: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 49.04 % | ||||||||||||||||||||
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1 microliter of VP1 at 10 mg/ml in 25 mM Na-HEPES, pH 7.8, 100 mM NaCl mixed with 2 microliter of crystallization buffer [25 mM Na-MES, pH 6.5, 1.5% (w/v) PEG 3350] and allowing the drop to ...Details: 1 microliter of VP1 at 10 mg/ml in 25 mM Na-HEPES, pH 7.8, 100 mM NaCl mixed with 2 microliter of crystallization buffer [25 mM Na-MES, pH 6.5, 1.5% (w/v) PEG 3350] and allowing the drop to equilibrate at 12 C by hanging-drop vapor diffusion with a well solution identical in composition to the drop except for the protein. With micro-seeding, thin, plate-like crystals appeared after 1 day and grew to full size in about two weeks., pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 285K | ||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 23, 2006 / Details: Undulator A | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 2.8 % / Av σ(I) over netI: 17.8 / Number: 137198 / Rmerge(I) obs: 0.051 / Χ2: 1 / D res high: 2.8 Å / D res low: 30 Å / Num. obs: 48859 / % possible obs: 81.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2.8→30 Å / Num. obs: 49581 / % possible obs: 81.9 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.051 / Χ2: 0.997 / Net I/σ(I): 17.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing |
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Phasing MR | Cor.coef. Fo:Fc: 0.41 / Packing: 0.307
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2R7Q Resolution: 2.8→30 Å / σ(F): 0
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Solvent computation | Bsol: 38.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.904 Å2 | ||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→30 Å
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Refine LS restraints |
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Xplor file |
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