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Yorodumi- PDB-6ex9: Crystal Structure of HIV-1 Integrase Catalytic Core Domain with I... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ex9 | ||||||
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Title | Crystal Structure of HIV-1 Integrase Catalytic Core Domain with Inhibitor Peptide | ||||||
Components |
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Keywords | VIRAL PROTEIN / HIV-1 / Integrase / Retroviruses / Catalytic core | ||||||
Function / homology | Function and homology information integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus ...integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / viral life cycle / nucleotidyltransferase activity / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / Assembly Of The HIV Virion / retroviral ribonuclease H / exoribonuclease H / Budding and maturation of HIV virion / exoribonuclease H activity / protein processing / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / symbiont-mediated suppression of host gene expression / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / peptidase activity / viral nucleocapsid / aspartic-type endopeptidase activity / endonuclease activity / DNA recombination / nucleic acid binding / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / DNA binding / zinc ion binding / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.014 Å | ||||||
Authors | Galilee, M. / Alian, A. | ||||||
Citation | Journal: Biorxiv / Year: 2018 Title: Multimerization of HIV-1 integrase hinges on conserved SH3-docking platforms Authors: Galilee, M. / Alian, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ex9.cif.gz | 44.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ex9.ent.gz | 29.7 KB | Display | PDB format |
PDBx/mmJSON format | 6ex9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ex9_validation.pdf.gz | 427 KB | Display | wwPDB validaton report |
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Full document | 6ex9_full_validation.pdf.gz | 427.6 KB | Display | |
Data in XML | 6ex9_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | 6ex9_validation.cif.gz | 10.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ex/6ex9 ftp://data.pdbj.org/pub/pdb/validation_reports/ex/6ex9 | HTTPS FTP |
-Related structure data
Related structure data | 1bisS 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
#1: Protein | Mass: 16549.908 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0U5B5J2, UniProt: P04585*PLUS |
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#2: Protein/peptide | Mass: 2008.016 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#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: 3.04 Å3/Da / Density % sol: 59.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: 0.1 M Succinic acid, 15 % w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97933 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 20, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97933 Å / Relative weight: 1 |
Reflection | Resolution: 2.014→68.26 Å / Num. obs: 15682 / % possible obs: 99.97 % / Redundancy: 9.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.029 / Rrim(I) all: 0.067 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 2.014→2.086 Å / Rmerge(I) obs: 0.885 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 1524 / % possible all: 99.93 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BIS Resolution: 2.014→68.249 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.66 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.014→68.249 Å
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Refine LS restraints |
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LS refinement shell |
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