[English] 日本語
Yorodumi- PDB-7dbm: HIV-1 reverse transcriptase mutant Q151M/Y115F/F116Y/M184V:DNA:dG... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dbm | ||||||
---|---|---|---|---|---|---|---|
Title | HIV-1 reverse transcriptase mutant Q151M/Y115F/F116Y/M184V:DNA:dGTP ternary complex | ||||||
Components |
| ||||||
Keywords | TRANSFERASE/DNA / Entecavir 5'-triphosphate / HIV-1 / HBV / reverse transcriptase / drug resistance / TRANSFERASE-DNA complex / REPLICATION | ||||||
Function / homology | Function and homology information HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 / symbiont-mediated suppression of host gene expression / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / aspartic-type endopeptidase activity / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / 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 / metal ion binding Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 Human immunodeficiency virus type 1 synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å | ||||||
Authors | Yasutake, Y. / Hattori, S.I. / Tamura, N. / Maeda, K. | ||||||
Funding support | Japan, 1items
| ||||||
Citation | Journal: J.Virol. / Year: 2021 Title: Biochemical and Structural Properties of Entecavir-Resistant Hepatitis B Virus Polymerase with L180M/M204V Mutations. Authors: Nakajima, S. / Watashi, K. / Kato, T. / Muramatsu, M. / Wakita, T. / Tamura, N. / Hattori, S.I. / Maeda, K. / Mitsuya, H. / Yasutake, Y. / Toyoda, T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7dbm.cif.gz | 891.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7dbm.ent.gz | 731.5 KB | Display | PDB format |
PDBx/mmJSON format | 7dbm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dbm_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7dbm_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7dbm_validation.xml.gz | 76.4 KB | Display | |
Data in CIF | 7dbm_validation.cif.gz | 103.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/db/7dbm ftp://data.pdbj.org/pub/pdb/validation_reports/db/7dbm | HTTPS FTP |
-Related structure data
Related structure data | 7dbnC 6kdnS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 64001.324 Da / Num. of mol.: 2 / Mutation: Q250M,Y214F,F215Y,M283V,C261S,C379S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Plasmid: pCDF / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL References: UniProt: D3XFN5, RNA-directed DNA polymerase, retroviral ribonuclease H #2: Protein | Mass: 51861.547 Da / Num. of mol.: 2 / Mutation: C749S,C867S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: P12497 |
---|
-DNA chain , 1 types, 2 molecules EF
#3: DNA chain | Mass: 11724.502 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
---|
-Non-polymers , 4 types, 448 molecules
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-GOL / #7: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.34 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: BIS-TRIS-HCL, DI-AMMONIUM HYDROGEN CITRATE, MGCL2, PEG 6000, SUCROSE, GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 18, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.43→50 Å / Num. obs: 107363 / % possible obs: 100 % / Redundancy: 5.4 % / Rrim(I) all: 0.103 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.43→2.47 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5360 / Rrim(I) all: 0.819 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6KDN Resolution: 2.43→48.469 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 23.06 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.43→48.469 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|