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Yorodumi- PDB-3oy9: Crystal structure of the Prototype Foamy Virus (PFV) intasome in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3oy9 | |||||||||
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Title | Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with manganese at 2.55 resolution | |||||||||
Components |
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Keywords | RECOMBINATION / VIRAL PROTEIN/DNA / PROTEIN-DNA COMPLEX / TETRAMER / DNA INTEGRATION / ENDONUCLEASE / METAL-BINDING / MULTIFUNCTIONAL ENZYME / NUCLEASE / NUCLEOTIDYLTRANSFERASE / NUCLEUS / TRANSFERASE / VIRAL NUCLEOPROTEIN / VIRION / DNA-BINDING / ZINC BINDING / HHCC MOTIF / VIRAL PROTEIN / DNA-BINDING PROTEIN-DNA complex / VIRAL PROTEIN-DNA complex | |||||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / DNA integration / virion component / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA-directed DNA polymerase activity / host cell ...Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / DNA integration / virion component / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / aspartic-type endopeptidase activity / DNA recombination / host cell cytoplasm / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont entry into host cell / host cell nucleus / proteolysis / RNA binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Human spumaretrovirus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | |||||||||
Authors | Hare, S. / Cherepanov, P. | |||||||||
Citation | Journal: Nature / Year: 2010 Title: Retroviral intasome assembly and inhibition of DNA strand transfer. Authors: Hare, S. / Gupta, S.S. / Valkov, E. / Engelman, A. / Cherepanov, P. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Molecular mechanisms of retroviral integrase inhibition and the evolution of viral resistance. Authors: Hare, S. / Vos, A.M. / Clayton, R.F. / Thuring, J.W. / Cummings, M.D. / Cherepanov, P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3oy9.cif.gz | 156.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3oy9.ent.gz | 115.9 KB | Display | PDB format |
PDBx/mmJSON format | 3oy9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3oy9_validation.pdf.gz | 481.8 KB | Display | wwPDB validaton report |
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Full document | 3oy9_full_validation.pdf.gz | 489.9 KB | Display | |
Data in XML | 3oy9_validation.xml.gz | 26.1 KB | Display | |
Data in CIF | 3oy9_validation.cif.gz | 37.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oy/3oy9 ftp://data.pdbj.org/pub/pdb/validation_reports/oy/3oy9 | HTTPS FTP |
-Related structure data
Related structure data | 3l2qC 3l2rSC 3l2uC 3l2vC 3l2wC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 44456.695 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human spumaretrovirus / Strain: HSRV2 / Gene: POL / Plasmid: pSSH6P-PFV-INFL / Production host: Escherichia coli (E. coli) / Strain (production host): PC2 / References: UniProt: P14350 |
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-DNA chain , 2 types, 2 molecules CD
#2: DNA chain | Mass: 5834.794 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Donor DNA non-transferred strand |
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#3: DNA chain | Mass: 5195.399 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Donor DNA transferred strand |
-Non-polymers , 6 types, 285 molecules
#4: Chemical | ChemComp-ZN / | ||||||||
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#5: Chemical | #6: Chemical | #7: Chemical | ChemComp-GOL / #8: Chemical | ChemComp-NH4 / | #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.97 Å3/Da / Density % sol: 69.04 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.35 M ammonium sulfate, 25% (v/v) glycerol, 4.8% (v/v) 1,6-hexanediol, 50 mM Mes-NaOH, 1mM EDTA, pH 6.5, vapor diffusion, hanging drop, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC / Detector: AREA DETECTOR / Date: Apr 26, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.55→39.206 Å / Num. obs: 52142 / % possible obs: 98.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Rsym value: 0.084 / Net I/σ(I): 14.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3L2R Resolution: 2.55→39.21 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 1 / SU B: 6.574 / SU ML: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 135.91 Å2 / Biso mean: 58.3457 Å2 / Biso min: 24.79 Å2
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Refinement step | Cycle: LAST / Resolution: 2.55→39.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.55→2.616 Å / Total num. of bins used: 20
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