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Yorodumi- PDB-4puo: Crystal structure of HIV-1 reverse transcriptase in complex with ... -
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-Basic information
Entry | Database: PDB / ID: 4puo | ||||||
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Title | Crystal structure of HIV-1 reverse transcriptase in complex with RNA/DNA and Nevirapine | ||||||
Components |
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Keywords | TRANSFERASE / HYDROLASE/DNA/RNA/INHIBITOR / fingers / palm / thumb / connection / RNase H / nucleotidyltransferase / DNA-directed DNA polymerase / RNA-directed DNA polymerase / Nuclease / Ribonuclease H / tRNA / HYDROLASE-DNA-RNA-INHIBITOR complex | ||||||
Function / homology | Function and homology information HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / 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 / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus type 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.901 Å | ||||||
Authors | Das, K. / Martinez, S.E. / Arnold, E. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2014 Title: Structures of HIV-1 RT-RNA/DNA ternary complexes with dATP and nevirapine reveal conformational flexibility of RNA/DNA: insights into requirements for RNase H cleavage. Authors: Das, K. / Martinez, S.E. / Bandwar, R.P. / Arnold, E. #1: Journal: Nat.Struct.Mol.Biol. / Year: 2012 Title: HIV-1 reverse transcriptase complex with DNA and nevirapine reveals non-nucleoside inhibition mechanism. Authors: Das, K. / Martinez, S.E. / Bauman, J.D. / Arnold, E. #2: Journal: J.Biol.Chem. / Year: 2009 Title: Structural basis for the role of the K65R mutation in HIV-1 reverse transcriptase polymerization, excision antagonism, and tenofovir resistance. Authors: Das, K. / Bandwar, R.P. / White, K.L. / Feng, J.Y. / Sarafianos, S.G. / Tuske, S. / Tu, X. / Clark, A.D. / Boyer, P.L. / Hou, X. / Gaffney, B.L. / Jones, R.A. / Miller, M.D. / Hughes, S.H. / Arnold, E. #3: Journal: Nat.Struct.Mol.Biol. / Year: 2010 Title: Structural basis of HIV-1 resistance to AZT by excision. Authors: Tu, X. / Das, K. / Han, Q. / Bauman, J.D. / Clark, A.D. / Hou, X. / Frenkel, Y.V. / Gaffney, B.L. / Jones, R.A. / Boyer, P.L. / Hughes, S.H. / Sarafianos, S.G. / Arnold, E. #4: Journal: Proc.Natl.Acad.Sci.USA / Year: 2008 Title: High-resolution structures of HIV-1 reverse transcriptase/TMC278 complexes: strategic flexibility explains potency against resistance mutations. Authors: Das, K. / Bauman, J.D. / Clark, A.D. / Frenkel, Y.V. / Lewi, P.J. / Shatkin, A.J. / Hughes, S.H. / Arnold, E. #5: Journal: Embo J. / Year: 2001 Title: Crystal structure of HIV-1 reverse transcriptase in complex with a polypurine tract RNA:DNA. Authors: Sarafianos, S.G. / Das, K. / Tantillo, C. / Clark, A.D. / Ding, J. / Whitcomb, J.M. / Boyer, P.L. / Hughes, S.H. / Arnold, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4puo.cif.gz | 448.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4puo.ent.gz | 356.3 KB | Display | PDB format |
PDBx/mmJSON format | 4puo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pu/4puo ftp://data.pdbj.org/pub/pdb/validation_reports/pu/4puo | HTTPS FTP |
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-Related structure data
Related structure data | 4pquC 4pwdC 4q0bC 3v81S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 64022.414 Da / Num. of mol.: 2 / Fragment: UNP residues 600-1153 / Mutation: Q258C, C280S, D498N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: BH10 / Gene: gag-pol / Production host: Escherichia coli (E. coli) References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H #2: Protein | Mass: 50039.488 Da / Num. of mol.: 2 / Fragment: UNP residues 600-1027 / Mutation: C280S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: BH10 / Gene: gag-pol / Production host: Escherichia coli (E. coli) References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase #3: RNA chain | Mass: 8759.271 Da / Num. of mol.: 2 / Source method: obtained synthetically #4: DNA chain | Mass: 6416.122 Da / Num. of mol.: 2 / Source method: obtained synthetically #5: Chemical | |
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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: 3.2 Å3/Da / Density % sol: 61.56 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: 9-11% PEG8000, 100 mM ammonium sulfate, 5% glycerol, 5% sucrose, 20 mM magnesium chloride, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.915 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 11, 2013 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.915 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 71012 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -1 / Redundancy: 3.5 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2.9→2.95 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.687 / Mean I/σ(I) obs: 1.27 / Num. unique all: 3336 / % possible all: 94.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3V81 Resolution: 2.901→46.508 Å / SU ML: 0.51 / σ(F): 0 / Phase error: 30.7 / 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: 2.901→46.508 Å
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Refine LS restraints |
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LS refinement shell |
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