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Yorodumi- PDB-4pqu: Crystal structure of HIV-1 Reverse Transcriptase in complex with ... -
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-Basic information
Entry | Database: PDB / ID: 4pqu | ||||||
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Title | Crystal structure of HIV-1 Reverse Transcriptase in complex with RNA/DNA and dATP | ||||||
Components |
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Keywords | TRANSFERASE / HYDROLASE/DNA/RNA / fingers / palm / thumb / connection / RNase H / nucleotidyltransferase / DNA-directed DNA polymerase / RNA-directed DNA polymerase / HYDROLASE-DNA-RNA complex | ||||||
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 / 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 / viral nucleocapsid / aspartic-type endopeptidase activity / DNA recombination / 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 / proteolysis / DNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus type 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.508 Å | ||||||
Authors | Das, K. / Bandwar, R.P. / 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 | 4pqu.cif.gz | 461.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pqu.ent.gz | 363.9 KB | Display | PDB format |
PDBx/mmJSON format | 4pqu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pqu_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 4pqu_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 4pqu_validation.xml.gz | 78 KB | Display | |
Data in CIF | 4pqu_validation.cif.gz | 108.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pq/4pqu ftp://data.pdbj.org/pub/pdb/validation_reports/pq/4pqu | HTTPS FTP |
-Related structure data
Related structure data | 4puoC 4pwdC 4q0bC 3v4iS 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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2 |
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Unit cell |
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-Components
-HIV-1 Reverse Transcriptase, ... , 2 types, 4 molecules ACBD
#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 |
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-RNA chain / DNA chain , 2 types, 4 molecules TEPF
#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 |
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-Non-polymers , 6 types, 451 molecules
#5: Chemical | #6: Chemical | ChemComp-MG / #7: Chemical | ChemComp-EDO / | #8: Chemical | ChemComp-SO4 / #9: Chemical | ChemComp-GOL / | #10: Water | ChemComp-HOH / | |
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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: 2.84 Å3/Da / Density % sol: 56.69 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG8000, Bis-tris propane, magnesium chloride, ammonium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING 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: Oct 30, 2009 |
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: 2.5→50 Å / Num. obs: 96955 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -1 / Redundancy: 3.6 % / Rmerge(I) obs: 0.102 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 3 % / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 1.84 / Num. unique all: 4765 / % possible all: 96.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3V4I Resolution: 2.508→40.468 Å / SU ML: 0.38 / σ(F): 1.39 / Phase error: 27.76 / Stereochemistry target values: Engh & Huber
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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: 2.508→40.468 Å
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Refine LS restraints |
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LS refinement shell |
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