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Yorodumi- PDB-4lh4: Dual inhibition of HIV-1 replication by Integrase-LEDGF allosteri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lh4 | ||||||
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Title | Dual inhibition of HIV-1 replication by Integrase-LEDGF allosteric inhibitors is predominant at post-integration stage during virus production rather than at integration | ||||||
Components | Integrase | ||||||
Keywords | TRANSFERASE / integrase | ||||||
Function / homology | Function and homology information HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / symbiont-mediated suppression of host gene expression / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / endonuclease activity / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / viral translational frameshifting / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Ruff, M. / Levy, N. / Eiler, S. | ||||||
Citation | Journal: Retrovirology / Year: 2013 Title: Dual inhibition of HIV-1 replication by integrase-LEDGF allosteric inhibitors is predominant at the post-integration stage. Authors: Le Rouzic, E. / Bonnard, D. / Chasset, S. / Bruneau, J.M. / Chevreuil, F. / Le Strat, F. / Nguyen, J. / Beauvoir, R. / Amadori, C. / Brias, J. / Vomscheid, S. / Eiler, S. / Levy, N. / ...Authors: Le Rouzic, E. / Bonnard, D. / Chasset, S. / Bruneau, J.M. / Chevreuil, F. / Le Strat, F. / Nguyen, J. / Beauvoir, R. / Amadori, C. / Brias, J. / Vomscheid, S. / Eiler, S. / Levy, N. / Delelis, O. / Deprez, E. / Saib, A. / Zamborlini, A. / Emiliani, S. / Ruff, M. / Ledoussal, B. / Moreau, F. / Benarous, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lh4.cif.gz | 46.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lh4.ent.gz | 31 KB | Display | PDB format |
PDBx/mmJSON format | 4lh4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4lh4_validation.pdf.gz | 436.1 KB | Display | wwPDB validaton report |
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Full document | 4lh4_full_validation.pdf.gz | 438.5 KB | Display | |
Data in XML | 4lh4_validation.xml.gz | 10 KB | Display | |
Data in CIF | 4lh4_validation.cif.gz | 13.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lh/4lh4 ftp://data.pdbj.org/pub/pdb/validation_reports/lh/4lh4 | HTTPS FTP |
-Related structure data
Related structure data | 4lh5C 1bhlS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 20139.646 Da / Num. of mol.: 1 / Fragment: UNP residues 50-212 / Mutation: F185K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9WJM2, UniProt: P12497*PLUS |
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#2: Chemical | ChemComp-MG / |
#3: 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: 2.45 Å3/Da / Density % sol: 49.74 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.16-1.36 M ammonium sulfate, 50 mM sodium cacodylate-HCl pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9191 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 10, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9191 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→28.27 Å / Num. obs: 16757 / % possible obs: 88.7 % / Rmerge(I) obs: 0.039 |
Reflection shell | Resolution: 1.8→1.96 Å / Redundancy: 5.17 % / Rmerge(I) obs: 0.141 / Mean I/σ(I) obs: 6.76 / Num. unique all: 3469 / % possible all: 65 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1BHL Resolution: 1.8→28.27 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.035 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.503 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→28.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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