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Yorodumi- PDB-3jyt: K65R mutant HIV-1 reverse transcriptase cross-linked to DS-DNA an... -
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-Basic information
Entry | Database: PDB / ID: 3jyt | |||||||||
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Title | K65R mutant HIV-1 reverse transcriptase cross-linked to DS-DNA and complexed with DATP as the incoming nucleotide substrate | |||||||||
Components |
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Keywords | TRANSFERASE/DNA COMPLEX / HIV-1 REVERSE TRANSCRIPTASE / TENOFOVIR / RT-DNA COMPLEX / TRANSFERASE-DNA COMPLEX / DRUG RESISTANCE MUTATION / AIDS / DNA RECOMBINATION / DNA-DIRECTED DNA POLYMERASE / RNASE H / HYDROLASE / LIPOPROTEIN / MAGNESIUM / MEMBRANE / METAL-BINDING / MULTIFUNCTIONAL ENZYME / NUCLEOTIDYLTRANSFERASE / RNA-DIRECTED DNA POLYMERASE TRANSFERASE / TRANSFERASE-DNA COMPLEX complex | |||||||||
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 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: 3.3 Å | |||||||||
Authors | Das, K. / Arnold, E. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Structural basis for the role of the K65r mutation in HIV-1 reverse transcriptase polymerization, excision antagonism, and tenofovir resistance. Authors: Das, K. / Bandwar, R.P. / White, K.L. / Feng, J.Y. / Sarafianos, S.G. / Tuske, S. / Tu, X. / Clark, A.D. / Boyer, P.L. / Hou, X. / Gaffney, B.L. / Jones, R.A. / Miller, M.D. / Hughes, S.H. / Arnold, E. #1: Journal: Nat.Struct.Mol.Biol. / Year: 2004 Title: Structures of HIV-1 RT-DNA Complexes Before and After Incorporation of the Anti-Aids Drug Tenofovir Authors: Tuske, S. / Sarafianos, S.G. / Clark Jr., A.D. / Ding, J. / Naeger, L.K. / White, K.L. / Miller, M.D. / Gibbs, C.S. / Boyer, P.L. / Clark, P. / Wang, G. / Gaffney, B.L. / Jones, R.A. / ...Authors: Tuske, S. / Sarafianos, S.G. / Clark Jr., A.D. / Ding, J. / Naeger, L.K. / White, K.L. / Miller, M.D. / Gibbs, C.S. / Boyer, P.L. / Clark, P. / Wang, G. / Gaffney, B.L. / Jones, R.A. / Jerina, D.M. / Hughes, S.H. / Arnold, E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3jyt.cif.gz | 235.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3jyt.ent.gz | 183.2 KB | Display | PDB format |
PDBx/mmJSON format | 3jyt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3jyt_validation.pdf.gz | 826.3 KB | Display | wwPDB validaton report |
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Full document | 3jyt_full_validation.pdf.gz | 913.5 KB | Display | |
Data in XML | 3jyt_validation.xml.gz | 48.5 KB | Display | |
Data in CIF | 3jyt_validation.cif.gz | 65.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jy/3jyt ftp://data.pdbj.org/pub/pdb/validation_reports/jy/3jyt | HTTPS FTP |
-Related structure data
Related structure data | 3jsmSC 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: 64277.676 Da / Num. of mol.: 1 / Mutation: K65R, Q258C, C280S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate BH10) Strain: isolate BH10 / Gene: gag-pol / Production host: Escherichia coli (E. coli) / Strain (production host): DH5ALPHA / References: UniProt: P03366, RNA-directed DNA polymerase |
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#2: Protein | Mass: 51095.617 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 BH10) Strain: isolate BH10 / Gene: gag-pol / Production host: Escherichia coli (E. coli) / Strain (production host): DH5ALPHA / References: UniProt: P03366 |
-DNA chain , 2 types, 2 molecules TP
#3: DNA chain | Mass: 8383.385 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Chemically modified with thiol-DGMP and enzymatically terminated with DDGTP Source: (synth.) synthetic construct (others) |
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#4: DNA chain | Mass: 6474.268 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 5 molecules
#5: Chemical | ChemComp-DTP / | ||
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#6: Chemical | #7: Chemical | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 4.96 Å3/Da / Density % sol: 75.21 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 10% PEG 8000, 100 MM AMMONIUM SULFATE, 20 MM MGCL2, 5% GLYCEROL, 5% SUCROSE, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 3.3→50 Å / Num. obs: 37809 / % possible obs: 98.6 % / Observed criterion σ(I): -1 / Rmerge(I) obs: 0.19 / Net I/σ(I): 8.6 | ||||||||||||||||||||||||
Reflection shell | Resolution: 3.3→3.42 Å / Rmerge(I) obs: 0.724 / % possible all: 87.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3JSM Resolution: 3.3→48.86 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 4288415.66 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 70.55 Å2 / ksol: 0.3 e/Å3 | |||||||||||||||||||||||||
Displacement parameters |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.3→48.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.3→3.51 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
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Xplor file |
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