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Yorodumi- PDB-8jyi: Crystal structure of engineered HIV-1 Reverse Transcriptase RNase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8jyi | ||||||
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Title | Crystal structure of engineered HIV-1 Reverse Transcriptase RNase H domain complexed with laccaic acid E | ||||||
Components | Pol protein,Pol protein,Ribonuclease H | ||||||
Keywords | VIRAL PROTEIN / Inhibitor | ||||||
Function / homology | Function and homology information DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / peptidase activity / DNA recombination / nucleic acid binding / aspartic-type endopeptidase activity / symbiont entry into host cell ...DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / peptidase activity / DNA recombination / nucleic acid binding / aspartic-type endopeptidase activity / symbiont entry into host cell / proteolysis / DNA binding / zinc ion binding / metal ion binding Similarity search - Function | ||||||
Biological species | HIV-1 06TG.HT008 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å | ||||||
Authors | Ito, Y. / Lu, H. / Kitajima, M. / Ishikawa, H. / Nakata, Y. / Iwatani, Y. / Hoshino, T. | ||||||
Funding support | 1items
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Citation | Journal: J.Nat.Prod. / Year: 2023 Title: Sticklac-Derived Natural Compounds Inhibiting RNase H Activity of HIV-1 Reverse Transcriptase. Authors: Ito, Y. / Lu, H. / Kitajima, M. / Ishikawa, H. / Nakata, Y. / Iwatani, Y. / Hoshino, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8jyi.cif.gz | 76.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jyi.ent.gz | 54.9 KB | Display | PDB format |
PDBx/mmJSON format | 8jyi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jy/8jyi ftp://data.pdbj.org/pub/pdb/validation_reports/jy/8jyi | HTTPS FTP |
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-Related structure data
Related structure data | 8jyhC 8jyjC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16832.285 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HIV-1 06TG.HT008 (virus) / Gene: pol, rnhA, ERS008198_04809, ERS008207_01536 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A059PIR4, UniProt: A0A1D9J5E8, ribonuclease H | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-V9O / | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.72 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.6 Details: 0.1M MES, 26%(v/v) PEG6000, 0.01 M Zinc Sulfate, 0.001 M MANGANESE CHLORIDE |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 27, 2022 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→43.62 Å / Num. obs: 12860 / % possible obs: 99.9 % / Redundancy: 12.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.015 / Rrim(I) all: 0.053 / Net I/σ(I): 21.5 / Num. measured all: 163286 |
Reflection shell | Resolution: 1.92→1.97 Å / % possible obs: 99.2 % / Redundancy: 12.5 % / Rmerge(I) obs: 0.985 / Num. measured all: 10472 / Num. unique obs: 835 / CC1/2: 0.664 / Rpim(I) all: 0.287 / Rrim(I) all: 1.027 / Net I/σ(I) obs: 1.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→43.62 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 0.04 / Phase error: 26.25 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.92→43.62 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 9.0384 Å / Origin y: 14.3033 Å / Origin z: 14.878 Å
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Refinement TLS group | Selection details: all |