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- PDB-3v6d: Crystal structure of HIV-1 reverse transcriptase (RT) cross-linke... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3v6d | ||||||
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Title | Crystal structure of HIV-1 reverse transcriptase (RT) cross-linked with AZT-terminated DNA | ||||||
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![]() | 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 | ||||||
Function / homology | ![]() HIV-1 retropepsin / 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 ...HIV-1 retropepsin / 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 / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Das, K. / Martinez, S.E. / Arnold, E. | ||||||
![]() | ![]() 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: ![]() 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: ![]() 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: ![]() 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: ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 451.7 KB | Display | ![]() |
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PDB format | ![]() | 358.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 516.2 KB | Display | ![]() |
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Full document | ![]() | 599.1 KB | Display | |
Data in XML | ![]() | 75.7 KB | Display | |
Data in CIF | ![]() | 101.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3v4iC ![]() 3v81C ![]() 3jsmS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: gag-pol / Production host: ![]() ![]() 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.) ![]() Gene: gag-pol / Production host: ![]() ![]() References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase #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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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.23 Å3/Da / Density % sol: 61.94 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 6.8 Details: PEG 8000, ammonium sulfate, sucrose, glycerol, magnesium chloride, pH 6.8, VAPOR DIFFUSION, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 1, 2011 / Details: MIRROR | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Rh coated Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→50 Å / Num. obs: 86184 / % possible obs: 98.4 % / Observed criterion σ(I): -1 / Redundancy: 3.9 % / Rmerge(I) obs: 0.089 / Χ2: 1.569 / Net I/σ(I): 11.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3JSM Resolution: 2.7048→44.3 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.776 / SU ML: 0.89 / σ(F): 1.39 / Phase error: 29.65 / 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: 58.761 Å2 / ksol: 0.321 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 179.72 Å2 / Biso mean: 80.3305 Å2 / Biso min: 28.66 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7048→44.3 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: 19
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