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Yorodumi- PDB-1t03: HIV-1 reverse transcriptase crosslinked to tenofovir terminated t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1t03 | ||||||
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Title | HIV-1 reverse transcriptase crosslinked to tenofovir terminated template-primer (complex P) | ||||||
Components |
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Keywords | Transferase/Antibody/DNA / HIV-1 RT / tenofovir / RT-DNA complex / Transferase-Antibody-DNA COMPLEX | ||||||
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 / viral penetration into host nucleus / establishment of integrated proviral latency ...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 / viral penetration into host nucleus / establishment of integrated proviral latency / 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 / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Tuske, S. / Sarafianos, S.G. / Ding, J. / Arnold, E. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2004 Title: Structure 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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Remark 999 | SEQUENCE The sequence of the FAB heavy and light chains are not available in any of the database ...SEQUENCE The sequence of the FAB heavy and light chains are not available in any of the database sequence. RESIDUE MRG 817 OF THE P CHAIN IS CROSSLINKED TO CHAIN A RESIDUE C258. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1t03.cif.gz | 323.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1t03.ent.gz | 254.2 KB | Display | PDB format |
PDBx/mmJSON format | 1t03.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1t03_validation.pdf.gz | 491.5 KB | Display | wwPDB validaton report |
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Full document | 1t03_full_validation.pdf.gz | 587.9 KB | Display | |
Data in XML | 1t03_validation.xml.gz | 63 KB | Display | |
Data in CIF | 1t03_validation.cif.gz | 86.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t0/1t03 ftp://data.pdbj.org/pub/pdb/validation_reports/t0/1t03 | HTTPS FTP |
-Related structure data
Related structure data | 1t05C 1n5yS 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
-Synthetic oligonucleotide ... , 2 types, 2 molecules TP
#1: DNA chain | Mass: 8367.386 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 6430.258 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Protein , 2 types, 2 molecules AB
#3: Protein | Mass: 64249.660 Da / Num. of mol.: 1 / Fragment: Reverse transcriptase, p66 subunit / Mutation: Q258C, C280S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: POL / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, RNA-directed DNA polymerase |
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#4: Protein | Mass: 51095.617 Da / Num. of mol.: 1 / Fragment: Reverse transcriptase, p51 subunit / Mutation: C280S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: POL / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, RNA-directed DNA polymerase |
-Antibody , 2 types, 2 molecules LH
#5: Antibody | Mass: 23362.650 Da / Num. of mol.: 1 / Fragment: Fab light chain domain / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
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#6: Antibody | Mass: 24000.814 Da / Num. of mol.: 1 / Fragment: Fab heavy chain domain / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
-Non-polymers , 1 types, 1 molecules
#7: Chemical | ChemComp-MG / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.98 Å3/Da / Density % sol: 71 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 100 mM cacodylate, 33% ammonium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 108 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 21, 2001 |
Radiation | Monochromator: Bending magnet / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→40 Å / Num. obs: 63979 / % possible obs: 95 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 45 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 3.1→3.21 Å / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 1.6 / Num. unique all: 4741 / % possible all: 74.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1N5Y Resolution: 3.1→20 Å / Isotropic thermal model: isotropic / σ(F): 1.1 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.12 Å /
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