+Open data
-Basic information
Entry | Database: PDB / ID: 4zhr | ||||||
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Title | Structure of HIV-1 RT Q151M mutant | ||||||
Components |
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Keywords | TRANSFERASE / HIV-1 reverse transcriptase / closed conformation / Q151M | ||||||
Function / homology | Function and homology information 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 | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.601 Å | ||||||
Authors | Nakamura, A. / Tamura, N. / Yasutake, Y. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2015 Title: Structure of the HIV-1 reverse transcriptase Q151M mutant: insights into the inhibitor resistance of HIV-1 reverse transcriptase and the structure of the nucleotide-binding pocket of Hepatitis B virus polymerase. Authors: Nakamura, A. / Tamura, N. / Yasutake, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zhr.cif.gz | 207 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zhr.ent.gz | 162.1 KB | Display | PDB format |
PDBx/mmJSON format | 4zhr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4zhr_validation.pdf.gz | 434.6 KB | Display | wwPDB validaton report |
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Full document | 4zhr_full_validation.pdf.gz | 440.7 KB | Display | |
Data in XML | 4zhr_validation.xml.gz | 32.7 KB | Display | |
Data in CIF | 4zhr_validation.cif.gz | 44.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zh/4zhr ftp://data.pdbj.org/pub/pdb/validation_reports/zh/4zhr | HTTPS FTP |
-Related structure data
Related structure data | 1rthS S: Starting model for refinement |
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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
#1: Protein | Mass: 64677.332 Da / Num. of mol.: 1 / Mutation: Q151M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Plasmid: pCDF-Duet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL References: UniProt: P12497*PLUS, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H |
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#2: Protein | Mass: 51264.039 Da / Num. of mol.: 1 / Mutation: T215I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL References: UniProt: P12497*PLUS, RNA-directed DNA polymerase, DNA-directed DNA polymerase |
#3: Water | ChemComp-HOH / |
Sequence details | The gene encoding HIV-1 RT used in this study is originated from the HIV-1 clone pNL4-3 (GenBank ...The gene encoding HIV-1 RT used in this study is originated from the HIV-1 clone pNL4-3 (GenBank ID, M19921.2). |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 9% PEG 8000, 0.2M imidazole |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 44912 / % possible obs: 100 % / Redundancy: 10 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.787 / Mean I/σ(I) obs: 2.1 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RTH Resolution: 2.601→47.704 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.41 / 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: 2.601→47.704 Å
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Refine LS restraints |
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LS refinement shell |
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