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Yorodumi- PDB-3v4i: Crystal structure of HIV-1 reverse transcriptase (RT) with DNA an... -
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-Basic information
Entry | Database: PDB / ID: 3v4i | ||||||
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Title | Crystal structure of HIV-1 reverse transcriptase (RT) with DNA and AZTTP | ||||||
Components |
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Keywords | TRANSFERASE/DNA / HIV-1 reverse transcriptase / zidovudine / RT-DNA complex / transferase-dna complex / drug resistance mutation / AIDS / DNA recombination / DNA-directed DNA polymerase / RNASE H / hydrolase / lipoprotein / magnesium / membrane / metal-binding / multifunctional enzyme / nucleotidyltransferase / RNA-directed DNA polymerase transferase / transferase-DNA complex 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 BH10 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7983 Å | ||||||
Authors | Das, K. / Martinez, S.E. / Arnold, E. | ||||||
Citation | 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. #1: 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. #2: 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. #3: 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. #4: Journal: J.Med.Chem. / Year: 2004 Title: Roles of conformational and positional adaptability in structure-based design of TMC125-R165335 (etravirine) and related non-nucleoside reverse transcriptase inhibitors that are highly potent ...Title: Roles of conformational and positional adaptability in structure-based design of TMC125-R165335 (etravirine) and related non-nucleoside reverse transcriptase inhibitors that are highly potent and effective against wild-type and drug-resistant HIV-1 variants. Authors: Das, K. / Clark, A.D. / Lewi, P.J. / Heeres, J. / De Jonge, M.R. / Koymans, L.M. / Vinkers, H.M. / Daeyaert, F. / Ludovici, D.W. / Kukla, M.J. / De Corte, B. / Kavash, R.W. / Ho, C.Y. / Ye, ...Authors: Das, K. / Clark, A.D. / Lewi, P.J. / Heeres, J. / De Jonge, M.R. / Koymans, L.M. / Vinkers, H.M. / Daeyaert, F. / Ludovici, D.W. / Kukla, M.J. / De Corte, B. / Kavash, R.W. / Ho, C.Y. / Ye, H. / Lichtenstein, M.A. / Andries, K. / Pauwels, R. / De Bethune, M.P. / Boyer, P.L. / Clark, P. / Hughes, S.H. / Janssen, P.A. / Arnold, E. #5: Journal: Science / Year: 1998 Title: Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: implications for drug resistance. Authors: Huang, H. / Chopra, R. / Verdine, G.L. / Harrison, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3v4i.cif.gz | 456 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3v4i.ent.gz | 361.9 KB | Display | PDB format |
PDBx/mmJSON format | 3v4i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3v4i_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3v4i_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 3v4i_validation.xml.gz | 78.4 KB | Display | |
Data in CIF | 3v4i_validation.cif.gz | 104.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v4/3v4i ftp://data.pdbj.org/pub/pdb/validation_reports/v4/3v4i | HTTPS FTP |
-Related structure data
Related structure data | 3v6dC 3v81C 3jsmS 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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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: D498N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 BH10 Gene: gag-pol / Production host: Escherichia coli (E. coli) References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase #2: Protein | Mass: 50039.488 Da / Num. of mol.: 2 / Fragment: UNP Residues 600-1027 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 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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-DNA chain , 2 types, 4 molecules TEPF
#3: DNA chain | Mass: 8416.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthesized #4: DNA chain | Mass: 6490.267 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthesized |
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-Non-polymers , 2 types, 4 molecules
#5: Chemical | #6: 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: 3.19 Å3/Da / Density % sol: 61.48 % |
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Crystal grow | Temperature: 277 K / Method: evaporation / pH: 6.8 Details: PEG 8000, AMMONIUM SULFATE, MGCL2, GLYCEROL, SUCROSE, pH 7.2, EVAPORATION, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 1, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 2.798→50 Å / Num. obs: 73202 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -1 / Redundancy: 3.2 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.798→2.9 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 1.9 / Num. unique all: 6702 / % possible all: 85.1 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3JSM Resolution: 2.7983→45.543 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7767 / SU ML: 0.98 / σ(F): 0 / Phase error: 29.62 / Stereochemistry target values: Engh & Huber
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.18 Å2 / ksol: 0.302 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 169.4 Å2 / Biso mean: 63.8603 Å2 / Biso min: 16.89 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7983→45.543 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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