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Yorodumi- PDB-6wpj: Structure of HIV-1 Reverse Transcriptase (RT) in complex with dsD... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wpj | ||||||
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Title | Structure of HIV-1 Reverse Transcriptase (RT) in complex with dsDNA and d4T | ||||||
Components |
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Keywords | TRANSFERASE/DNA / Reverse Transcriptase / ternary complex / d4T / chain terminator / stereochemistry / TRANSFERASE / TRANSFERASE-DNA complex / Stavudine | ||||||
Function / homology | Function and homology information integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus ...integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / viral life cycle / Assembly Of The HIV Virion / HIV-1 retropepsin / : / Budding and maturation of HIV virion / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / protein processing / host multivesicular body / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / peptidase activity / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / DNA binding / RNA binding / zinc ion binding / membrane / identical protein binding Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus type 1 group M subtype B synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å | ||||||
Authors | Bertoletti, N. / Anderson, K.S. | ||||||
Funding support | United States, 1items
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Citation | Journal: Molecules / Year: 2020 Title: Post-Catalytic Complexes with Emtricitabine or Stavudine and HIV-1 Reverse Transcriptase Reveal New Mechanistic Insights for Nucleotide Incorporation and Drug Resistance. Authors: Bertoletti, N. / Chan, A.H. / Schinazi, R.F. / Anderson, K.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wpj.cif.gz | 281.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wpj.ent.gz | 175.7 KB | Display | PDB format |
PDBx/mmJSON format | 6wpj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wp/6wpj ftp://data.pdbj.org/pub/pdb/validation_reports/wp/6wpj | HTTPS FTP |
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-Related structure data
Related structure data | 6wpfC 6wphC 6or7S 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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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 64653.090 Da / Num. of mol.: 1 / Mutation: C280S, Q258C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate HXB2) Strain: isolate HXB2 / Gene: gag-pol / Production host: Escherichia coli BL21 (bacteria) References: UniProt: P04585, 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.) Human immunodeficiency virus type 1 group M subtype B (isolate HXB2) Strain: isolate HXB2 / Gene: gag-pol / Production host: Escherichia coli BL21 (bacteria) References: UniProt: P04585, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, Hydrolases; Acting on ester bonds |
-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: 8392.398 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 4 types, 10 molecules
#5: Chemical | ChemComp-D4T / | ||||
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#6: Chemical | #7: Chemical | ChemComp-SO4 / | #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 2.74 Å3/Da / Density % sol: 55.21 % / Description: thin plates |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 6-10% (w/v) PEG 8000, 15 mM magnesium sulfate, and 50 mM MES adjusted at pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 11, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.73→50 Å / Num. obs: 38882 / % possible obs: 99.1 % / Redundancy: 7.2 % / Biso Wilson estimate: 62.72 Å2 / CC1/2: 0.996 / CC star: 0.996 / Rsym value: 0.153 / Net I/σ(I): 12.46 |
Reflection shell | Resolution: 2.73→2.9 Å / Redundancy: 6.69 % / Mean I/σ(I) obs: 1.56 / Num. unique obs: 5942 / CC1/2: 0.673 / CC star: 0.673 / Rsym value: 1.257 / % possible all: 94.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6OR7 Resolution: 2.73→47.56 Å / SU ML: 0.4529 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.011
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.58 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.73→47.56 Å
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Refine LS restraints |
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LS refinement shell |
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