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Yorodumi- PDB-3s3o: Crystal structure of the Prototype Foamy Virus (PFV) N224H mutant... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3s3o | ||||||
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Title | Crystal structure of the Prototype Foamy Virus (PFV) N224H mutant intasome in complex with magnesium and Dolutegravir (S/GSK1349572) | ||||||
Components |
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Keywords | RECOMBINATION/INHIBITOR/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 / RECOMBINATION / INHIBITOR / RECOMBINATION-INHIBITOR-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: Mol.Pharmacol. / Year: 2011 Title: Structural and Functional Analyses of the Second-Generation Integrase Strand Transfer Inhibitor Dolutegravir (S/GSK1349572). Authors: Hare, S. / Smith, S.J. / Metifiot, M. / Jaxa-Chamiec, A. / Pommier, Y. / Hughes, S.H. / Cherepanov, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3s3o.cif.gz | 156.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3s3o.ent.gz | 116.3 KB | Display | PDB format |
PDBx/mmJSON format | 3s3o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3s3o_validation.pdf.gz | 817 KB | Display | wwPDB validaton report |
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Full document | 3s3o_full_validation.pdf.gz | 826.5 KB | Display | |
Data in XML | 3s3o_validation.xml.gz | 25.4 KB | Display | |
Data in CIF | 3s3o_validation.cif.gz | 36.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s3/3s3o ftp://data.pdbj.org/pub/pdb/validation_reports/s3/3s3o | HTTPS FTP |
-Related structure data
Related structure data | 3s3mC 3s3nC 3oynS S: Starting model for refinement C: citing same article (ref.) |
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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: 44480.738 Da / Num. of mol.: 2 / Mutation: G968S, N975H 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, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases |
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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: 19 nucleotide preprocessed PFV 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: 17 nucleotide preprocessed PFV donor DNA (transferred strand) |
-Non-polymers , 8 types, 212 molecules
#4: Chemical | ChemComp-ZN / | ||||||||||||
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#5: Chemical | #6: Chemical | ChemComp-GOL / #7: Chemical | ChemComp-NH4 / | #8: Chemical | #9: Chemical | ChemComp-DLU / ( | #10: Chemical | ChemComp-HEZ / | #11: 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: 3.96 Å3/Da / Density % sol: 68.93 % |
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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: 0.9763 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 28, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.55→39.141 Å / Num. all: 52365 / Num. obs: 52365 / % possible obs: 99.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 8.6 % / Rsym value: 0.086 / Net I/σ(I): 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3OYN Resolution: 2.55→39.14 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.2246 / WRfactor Rwork: 0.2033 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8494 / SU B: 6.791 / SU ML: 0.147 / SU R Cruickshank DPI: 0.2379 / SU Rfree: 0.1975 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.197 / 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: 146.35 Å2 / Biso mean: 59.3555 Å2 / Biso min: 25.05 Å2
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Refinement step | Cycle: LAST / Resolution: 2.55→39.14 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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