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- PDB-4q0b: Crystal structure of HIV-1 reverse transcriptase in complex with ... -
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Basic information
Entry | Database: PDB / ID: 4q0b | ||||||
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Title | Crystal structure of HIV-1 reverse transcriptase in complex with gap-RNA/DNA and Nevirapine | ||||||
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![]() | TRANSFERASE / HYDROLASE/RNA/DNA/INHIBITOR / fingers / palm / thumb / connection / RNase H / nucleotidyltransferase / DNA-directed DNA polymerase / RNA-directed DNA polymerase / ribonuclease H / tRNA / HYDROLASE-RNA-DNA-INHIBITOR complex | ||||||
Function / homology | ![]() 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 / 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: 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: ![]() 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: ![]() 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: ![]() 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: ![]() 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: ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 443.5 KB | Display | ![]() |
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PDB format | ![]() | 355.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4pquC ![]() 4puoC ![]() 4pwdC ![]() 3v81S 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
-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.) ![]() ![]() ![]() ![]() 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.) ![]() ![]() ![]() ![]() References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase |
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-RNA chain , 2 types, 4 molecules TEte
#3: RNA chain | Mass: 4493.724 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: gap-RNA template #4: RNA chain | Mass: 3891.384 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: gap-RNA template |
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-DNA chain , 1 types, 2 molecules PF
#5: DNA chain | Mass: 6416.122 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA primer |
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-Non-polymers , 3 types, 5 molecules ![](data/chem/img/NVP.gif)
![](data/chem/img/MN.gif)
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#6: Chemical | #7: Chemical | #8: Chemical | ChemComp-SO4 / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.14 % |
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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: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 13, 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: 3.3→50 Å / Num. all: 49011 / Num. obs: 48325 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -1 / Redundancy: 3 % / Rmerge(I) obs: 0.142 / Net I/σ(I): 7 |
Reflection shell | Resolution: 3.3→3.36 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 1.38 / Num. unique all: 2355 / % possible all: 97.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3V81 Resolution: 3.3→46.391 Å / SU ML: 0.62 / σ(F): 0 / Phase error: 34.62 / 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: 3.3→46.391 Å
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Refine LS restraints |
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LS refinement shell |
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