+Open data
-Basic information
Entry | Database: PDB / ID: 1tvr | ||||||
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Title | HIV-1 RT/9-CL TIBO | ||||||
Components | (REVERSE TRANSCRIPTASE) x 2 | ||||||
Keywords | ASPARTYL PROTEASE / AIDS / POLYPROTEIN / HYDROLASE / ENDONUCLEASE / RNA-DIRECTED DNA POLYMERASE / 3HIV-1 RT/9-CL TIBO | ||||||
Function / homology | Function and homology information : / : / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...: / : / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / 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 / RNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus type 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å | ||||||
Authors | Das, K. / Ding, J. / Hsiou, Y. / Arnold, E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1996 Title: Crystal structures of 8-Cl and 9-Cl TIBO complexed with wild-type HIV-1 RT and 8-Cl TIBO complexed with the Tyr181Cys HIV-1 RT drug-resistant mutant. Authors: Das, K. / Ding, J. / Hsiou, Y. / Clark Jr., A.D. / Moereels, H. / Koymans, L. / Andries, K. / Pauwels, R. / Janssen, P.A. / Boyer, P.L. / Clark, P. / Smith Jr., R.H. / Kroeger Smith, M.B. / ...Authors: Das, K. / Ding, J. / Hsiou, Y. / Clark Jr., A.D. / Moereels, H. / Koymans, L. / Andries, K. / Pauwels, R. / Janssen, P.A. / Boyer, P.L. / Clark, P. / Smith Jr., R.H. / Kroeger Smith, M.B. / Michejda, C.J. / Hughes, S.H. / Arnold, E. #1: Journal: Drug Des.Discovery / Year: 1996 Title: Targeting HIV Reverse Transcriptase for Anti-Aids Drug Design: Structural and Biological Considerations for Chemotherapeutic Strategies Authors: Arnold, E. / Das, K. / Ding, J. / Yadav, P.N. / Hsiou, Y. / Boyer, P.L. / Hughes, S.H. #2: Journal: Structure / Year: 1996 Title: Structure of Unliganded HIV-1 Reverse Transcriptase at 2.7 A Resolution: Implications of Conformational Changes for Polymerization and Inhibition Mechanisms Authors: Hsiou, Y. / Ding, J. / Das, K. / Clark Junior, A.D. / Hughes, S.H. / Arnold, E. #3: Journal: Structure / Year: 1995 Title: Structure of HIV-1 Reverse Transcriptase in a Complex with the Non-Nucleoside Inhibitor Alpha-Apa R 95845 at 2.8 A Resolution Authors: Ding, J. / Das, K. / Tantillo, C. / Zhang, W. / Clark Junior, A.D. / Jessen, S. / Lu, X. / Hsiou, Y. / Jacobo-Molina, A. / Andries, K. / al., et #4: Journal: Nat.Struct.Biol. / Year: 1995 Title: Structure of HIV-1 RT/TIBO R 86183 Complex Reveals Similarity in the Binding of Diverse Nonnucleoside Inhibitors Authors: Ding, J. / Das, K. / Moereels, H. / Koymans, L. / Andries, K. / Janssen, P.A. / Hughes, S.H. / Arnold, E. #5: Journal: J.Mol.Biol. / Year: 1994 Title: Locations of Anti-Aids Drug Binding Sites and Resistance Mutations in the Three-Dimensional Structure of HIV-1 Reverse Transcriptase. Implications for Mechanisms of Drug Inhibition and Resistance Authors: Tantillo, C. / Ding, J. / Jacobo-Molina, A. / Nanni, R.G. / Boyer, P.L. / Hughes, S.H. / Pauwels, R. / Andries, K. / Janssen, P.A. / Arnold, E. #6: Journal: J.Mol.Recog. / Year: 1994 Title: Buried Surface Analysis of HIV-1 Reverse Transcriptase P66/P51 Heterodimer and its Interaction with DsDNA Template/Primer Authors: Ding, J. / Jacobo-Molina, A. / Tantillo, C. / Lu, X. / Nanni, R.G. / Arnold, E. #7: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993 Title: Crystal Structure of Human Immunodeficiency Virus Type 1 Reverse Transcriptase Complexed with Double-Stranded DNA at 3.0 A Resolution Shows Bent DNA Authors: Jacobo-Molina, A. / Ding, J. / Nanni, R.G. / Clark Junior, A.D. / Lu, X. / Tantillo, C. / Williams, R.L. / Kamer, G. / Ferris, A.L. / Clark, P. / al., et | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tvr.cif.gz | 204.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tvr.ent.gz | 162.4 KB | Display | PDB format |
PDBx/mmJSON format | 1tvr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tv/1tvr ftp://data.pdbj.org/pub/pdb/validation_reports/tv/1tvr | HTTPS FTP |
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-Related 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: 64274.652 Da / Num. of mol.: 1 / Mutation: C280S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 (CLONE 12) Genus: Lentivirus / Species: Human immunodeficiency virus 1Subtypes of HIV / Strain: BH10 Description: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 (HIV-1) SUBCLONED FROM BH10 ISOLATE. EXPRESSED AND PROCESSED BY BACTERIAL ESCHERICHIA COLI. REF. A.HIZI, ET AL., (1988) PROC. NATL. ACAD. SCI. USA 85, ...Description: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 (HIV-1) SUBCLONED FROM BH10 ISOLATE. EXPRESSED AND PROCESSED BY BACTERIAL ESCHERICHIA COLI. REF. A.HIZI, ET AL., (1988) PROC. NATL. ACAD. SCI. USA 85, 1218-1222. REF. P.K.CLARK, ET AL., (1990) AIDS RES. HUM. RETROVIRUSES 6, 753-764. Cell line: 293 / Production host: Escherichia coli (E. coli) / Strain (production host): 293 / References: UniProt: P03366, RNA-directed DNA polymerase |
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#2: Protein | Mass: 49911.359 Da / Num. of mol.: 1 / Mutation: C280S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 (CLONE 12) Genus: Lentivirus / Species: Human immunodeficiency virus 1Subtypes of HIV / Strain: BH10 Description: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 (HIV-1) SUBCLONED FROM BH10 ISOLATE. EXPRESSED AND PROCESSED BY BACTERIAL ESCHERICHIA COLI. REF. A.HIZI, ET AL., (1988) PROC. NATL. ACAD. SCI. USA 85, ...Description: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 (HIV-1) SUBCLONED FROM BH10 ISOLATE. EXPRESSED AND PROCESSED BY BACTERIAL ESCHERICHIA COLI. REF. A.HIZI, ET AL., (1988) PROC. NATL. ACAD. SCI. USA 85, 1218-1222. REF. P.K.CLARK, ET AL., (1990) AIDS RES. HUM. RETROVIRUSES 6, 753-764. Cell line: 293 / Production host: Escherichia coli (E. coli) / Strain (production host): 293 / References: UniProt: P03366, RNA-directed DNA polymerase |
#3: Chemical | ChemComp-TB9 / |
Compound details | HIV-1 RT IS COMPOSED OF TWO SUBUNITS OF 66 KDA AND 51 KDA, DESIGNATED AS P66 AND P51, RESPECTIVELY. ...HIV-1 RT IS COMPOSED OF TWO SUBUNITS OF 66 KDA AND 51 KDA, DESIGNATED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.41 Å3/Da / Density % sol: 65 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6.8 / Method: vapor diffusion, hanging drop / Details: Clark, A.D., (1995) Methods Enzymol., 262, 171. | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918 |
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Detector | Detector: CCD / Date: Nov 1, 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Num. obs: 26209 / % possible obs: 84 % / Observed criterion σ(I): 1 / Redundancy: 2.16 % / Rmerge(I) obs: 0.064 |
Reflection | *PLUS Highest resolution: 3 Å / Lowest resolution: 40 Å / Num. measured all: 56695 |
-Processing
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Refinement | Resolution: 3→10 Å / σ(F): 2 /
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Refine analyze | Luzzati coordinate error obs: 0.6 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |