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Yorodumi- PDB-7adv: Crystal structure of the Prototype Foamy Virus (PFV) intasome in ... -
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-Basic information
Entry | Database: PDB / ID: 7adv | ||||||
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Title | Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium and the INSTI XZ447 (compound 6v) | ||||||
Components |
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Keywords | VIRAL PROTEIN / Integrase / Intasome / Protein DNA complex / INSTI / Drug / HIV / Retrovirus / Integration | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / virion component / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases ...Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / virion component / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / DNA recombination / host cell cytoplasm / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / 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 synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Pye, V.E. / Cherepanov, P. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Acs Infect Dis. / Year: 2021 Title: HIV-1 Integrase Inhibitors with Modifications That Affect Their Potencies against Drug Resistant Integrase Mutants. Authors: Smith, S.J. / Zhao, X.Z. / Passos, D.O. / Pye, V.E. / Cherepanov, P. / Lyumkis, D. / Burke Jr., T.R. / Hughes, S.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7adv.cif.gz | 190.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7adv.ent.gz | 117.6 KB | Display | PDB format |
PDBx/mmJSON format | 7adv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ad/7adv ftp://data.pdbj.org/pub/pdb/validation_reports/ad/7adv | HTTPS FTP |
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-Related structure data
Related structure data | 7aduC 4bdzS 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: 44456.695 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human spumaretrovirus / Gene: pol / Production host: Escherichia coli (E. coli) References: UniProt: P14350, RNA-directed DNA polymerase, DNA-directed DNA polymerase, ribonuclease H, Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases, Transferases; ...References: UniProt: P14350, RNA-directed DNA polymerase, DNA-directed DNA polymerase, ribonuclease H, Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, Hydrolases; Acting on ester bonds |
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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 / Source: (synth.) synthetic construct (others) |
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#3: DNA chain | Mass: 5195.399 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 6 types, 188 molecules
#4: Chemical | #5: Chemical | ChemComp-ZN / | #6: Chemical | ChemComp-R7N / | #7: Chemical | ChemComp-SO4 / #8: Chemical | ChemComp-GOL / #9: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.87 Å3/Da / Density % sol: 68.2 % |
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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 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: cryo cooled / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97957 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 3, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97957 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→70.93 Å / Num. obs: 45907 / % possible obs: 99.7 % / Redundancy: 11.6 % / Biso Wilson estimate: 72.15 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.027 / Net I/σ(I): 20.8 |
Reflection shell | Resolution: 2.65→2.72 Å / Rmerge(I) obs: 1.701 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3274 / CC1/2: 0.521 / Rpim(I) all: 0.555 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4BDZ Resolution: 2.65→50.16 Å / SU ML: 0.3697 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.9271 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 73.35 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→50.16 Å
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Refine LS restraints |
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LS refinement shell |
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