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Yorodumi- PDB-6bsj: Structure of HIV-1 RT complexed with an RNA/DNA hybrid sequence n... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bsj | ||||||
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Title | Structure of HIV-1 RT complexed with an RNA/DNA hybrid sequence non-preferred for RNA hydrolysis | ||||||
Components |
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Keywords | viral protein/dna/rna/inhibitor / HIV-RT / DNA-RNA complex / RNase H / VIRAL PROTEIN / viral protein-dna-rna complex / viral protein-dna-rna-inhibitor complex | ||||||
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 / 2-LTR circle formation / Uncoating of the HIV Virion / 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 / 2-LTR circle formation / Uncoating of the HIV Virion / 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 / RNA stem-loop binding / viral life cycle / : / : / Assembly Of The HIV Virion / HIV-1 retropepsin / retroviral ribonuclease H / Budding and maturation of HIV virion / exoribonuclease H / exoribonuclease H activity / protein processing / host multivesicular body / DNA integration / 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 / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / peptidase activity / symbiont-mediated suppression of host gene expression / 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 / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane / identical protein binding Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.89 Å | ||||||
Authors | Tian, L. / Kim, M. / Yang, W. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018 Title: Structure of HIV-1 reverse transcriptase cleaving RNA in an RNA/DNA hybrid. Authors: Tian, L. / Kim, M.S. / Li, H. / Wang, J. / Yang, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bsj.cif.gz | 237.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bsj.ent.gz | 181.2 KB | Display | PDB format |
PDBx/mmJSON format | 6bsj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bs/6bsj ftp://data.pdbj.org/pub/pdb/validation_reports/bs/6bsj | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-REVERSE TRANSCRIPTASE ... , 2 types, 2 molecules AB
#1: Protein | Mass: 64126.395 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Production host: Escherichia coli (E. coli) / References: UniProt: Q74085, UniProt: P04585*PLUS |
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#2: Protein | Mass: 51384.031 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Production host: Escherichia coli (E. coli) / References: UniProt: A0A076Q3N8, UniProt: P04585*PLUS |
-DNA chain / RNA chain , 2 types, 2 molecules DR
#3: DNA chain | Mass: 7077.567 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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#4: RNA chain | Mass: 7903.798 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
-Non-polymers , 5 types, 24 molecules
#5: Chemical | ChemComp-EFZ / (-)- | ||||
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#6: Chemical | ChemComp-CA / | ||||
#7: Chemical | ChemComp-GOL / #8: Chemical | ChemComp-TAM / | #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.82 Å3/Da / Density % sol: 67.77 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: Sodium citrate pH 5.2, CaCl2, PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 10, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.89→41.2 Å / Num. obs: 44876 / % possible obs: 99.96 % / Redundancy: 7.4 % / Rsym value: 0.093 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2.89→2.97 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 1.96 / Num. unique obs: 4422 / % possible all: 99.98 |
-Processing
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Refinement | Resolution: 2.89→41.199 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.87 / 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: 2.89→41.199 Å
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Refine LS restraints |
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LS refinement shell |
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