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- PDB-6oun: Structure of HIV-1 Reverse Transcriptase (RT) in complex with dsD... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6oun | ||||||
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Title | Structure of HIV-1 Reverse Transcriptase (RT) in complex with dsDNA and (-)3TC-TP | ||||||
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![]() | TRANSFERASE/DNA / Reverse Transcriptase / ternary complex / (-)3TC-TP / chain terminator / lamivudine / stereochemistry / TRANSFERASE / TRANSFERASE-DNA complex | ||||||
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 | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bertoletti, N. / Anderson, K.S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insights into the recognition of nucleoside reverse transcriptase inhibitors by HIV-1 reverse transcriptase: First crystal structures with reverse transcriptase and the active ...Title: Structural insights into the recognition of nucleoside reverse transcriptase inhibitors by HIV-1 reverse transcriptase: First crystal structures with reverse transcriptase and the active triphosphate forms of lamivudine and emtricitabine. Authors: Bertoletti, N. / Chan, A.H. / Schinazi, R.F. / Yin, Y.W. / Anderson, K.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 439.5 KB | Display | ![]() |
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PDB format | ![]() | 352.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 765.3 KB | Display | ![]() |
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Full document | ![]() | 772.3 KB | Display | |
Data in XML | ![]() | 34.6 KB | Display | |
Data in CIF | ![]() | 47.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6or7C ![]() 6otzC ![]() 6p1iC ![]() 6p1xC ![]() 6p2gC ![]() 3kjvS S: Starting model for refinement C: citing same article ( |
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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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 64309.605 Da / Num. of mol.: 1 / Mutation: C280S, Q258C 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, retroviral ribonuclease H |
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#2: Protein | Mass: 52748.418 Da / Num. of mol.: 1 / Mutation: C280S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: isolate BH10 / Gene: gag-pol / Variant: isolate BH10 / Production host: ![]() ![]() |
-DNA chain , 2 types, 2 molecules PT
#3: DNA chain | Mass: 6460.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#4: DNA chain | Mass: 8408.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 4 types, 17 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/1RZ.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/1RZ.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | #6: Chemical | #7: Chemical | ChemComp-1RZ / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.43 % / Description: plates |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 3-6% (w/v) PEG 8000, 15 mM magnesium sulfate, and 50 mM MES adjusted at pH 6.0 PH range: 5.5-6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 7, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.656→30 Å / Num. obs: 44155 / % possible obs: 99.8 % / Redundancy: 26.3 % / CC1/2: 0.999 / Rsym value: 0.13 / Net I/σ(I): 19.54 |
Reflection shell | Resolution: 2.656→2.82 Å / Redundancy: 28.6 % / Mean I/σ(I) obs: 1.93 / Num. unique obs: 6977 / CC1/2: 0.92 / Rsym value: 1.48 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3KJV Resolution: 2.656→29.571 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.92 / 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: 2.656→29.571 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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