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Yorodumi- PDB-1ep4: Crystal structure of HIV-1 reverse transcriptase in complex with ... -
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Entry | Database: PDB / ID: 1ep4 | ||||||
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Title | Crystal structure of HIV-1 reverse transcriptase in complex with S-1153 | ||||||
Components | (HIV-1 REVERSE TRANSCRIPTASE) x 2 | ||||||
Keywords | TRANSFERASE / HIV-1 reverse transcriptase / AIDS / non-nucleoside inhibitor / S-1153 / drug design | ||||||
Function / homology | Function and homology information integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus ...integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / viral life cycle / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / Assembly Of The HIV Virion / retroviral ribonuclease H / exoribonuclease H / Budding and maturation of HIV virion / exoribonuclease H activity / protein processing / host multivesicular body / 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 / peptidase activity / 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 / structural molecule activity / virion membrane / DNA binding / zinc ion binding / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å | ||||||
Authors | Ren, J. / Nichols, C. / Bird, L.E. / Fujiwara, T. / Suginoto, H. / Stuart, D.I. / Stammers, D.K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2000 Title: Binding of the second generation non-nucleoside inhibitor S-1153 to HIV-1 reverse transcriptase involves extensive main chain hydrogen bonding. Authors: Ren, J. / Nichols, C. / Bird, L.E. / Fujiwara, T. / Sugimoto, H. / Stuart, D.I. / Stammers, D.K. #1: Journal: J.Biol.Chem. / Year: 2000 Title: Phenethylthiazolylthiourea (PETT) Non-nucleoside Inhibitors of HIV-1 and HIV-2 Reverse Transcriptases: Structural and Biochemical Analyses Authors: Ren, J. / Diprose, J. / Warren, J. / Esnouf, R.M. / Bird, L.E. / Ikemizu, S. / Slater, M. / Milton, J. / Balzarini, J. / Stuart, D.I. / Stammers, D.K. #2: Journal: J.Med.Chem. / Year: 1999 Title: Crystallographic Analysis of the Binding Modes of Non-nucleoside Thiazoloisoindolinone Inhibitors to HIV-1 Reverse Transcriptase and Comparison with Modeling Studies Authors: Ren, J. / Esnouf, R.M. / Hopkins, A.L. / Stuart, D.I. / Stammers, D.K. #3: Journal: J.Med.Chem. / Year: 1999 Title: Design of MKC-442 (emivirine) Analogues with Improved Activity Against Drug-resistant HIV Mutants Authors: Hopkins, A.L. / Ren, J. / Tanaka, H. / Baba, M. / Okamato, M. / Stuart, D.I. / Stammers, D.K. #4: Journal: Biochemistry / Year: 1998 Title: Crystal Structures of Reverse Transcriptase in Complex with Carboxanilide Derivatives Authors: Ren, J. / Esnouf, R.M. / Hopkins, A.L. / Warren, J. / Balzarini, J. / Stuart, D.I. / Stammers, D.K. #5: Journal: Proc.Natl.Acad.Sci.USA / Year: 1998 Title: 3'-azido-3'-deoxythymidine Drug Resistance Mutations in HIV-1 Reverse Transcriptase can Induce Long Range Conformational Changes Authors: Ren, J. / Esnouf, R.M. / Hopkins, A.L. / Jones, E.Y. / Kirby, I. / Keeling, J. / Ross, C.K. / Larder, B.A. / Stuart, D.I. / Stammers, D.K. #6: Journal: Acta Crystallogr.,Sect.D / Year: 1998 Title: Continuous and Discontinuous Changes in the Unit Cell of HIV-1 Reverse Transcriptase Crystals on Dehydration Authors: Esnouf, R.M. / Ren, J. / Garman, E.F. / Somers, D.O. / Ross, C.K. / Jones, E.Y. / Stammers, D.K. / Stuart, D.I. #7: Journal: Proc.Natl.Acad.Sci.USA / Year: 1997 Title: Unique Features in the Structure of the Complex Between HIV-1 Reverse Transcriptase and the Bis(heteroaryl)piperazine (BHAP) U-90152 Explain Resistance Mutations for this Non-nucleoside Inhibitor Authors: Esnouf, R.M. / Ren, J. / Hopkins, A.L. / Ross, C.K. / Jones, E.Y. / Stammers, D.K. / Stuart, D.I. #8: Journal: J.Med.Chem. / Year: 1996 Title: Complexes of HIV-1 Reverse Transcriptase with Inhibitors of the HEPT Series Reveal Conformational Changes Relevant to the Design of Potent Non-nucleoside Inhibitors Authors: L Hopkins, A. / Ren, J. / Esnouf, R.M. / Willcox, B.E. / Jones, E.Y. / Ross, C.K. / Miyasaka, T. / Walker, R.T. / Tanaka, H. / Stammers, D.K. / Stuart, D.I. #9: Journal: Structure / Year: 1995 Title: The Structure of HIV-1 Reverse Transcriptase Complexed with 9-chloro-TIBO: Lessons for Inhibitor Design Authors: Ren, J. / Esnouf, R.M. / Hopkins, A.L. / Ross, C.K. / Jones, E.Y. / K Stammers, D. / Stuart, D.I. #10: Journal: Nat.Struct.Biol. / Year: 1995 Title: High Resolution Structures of HIV-1 RT From Four RT-inhibitor Complexes Authors: Ren, J. / Esnouf, R.M. / Garman, E. / Somers, D.O. / Ross, C.K. / Kirby, I. / Keeling, J. / Darby, G. / Jones, E.Y. / Stuart, D.I. / Stammers, D.K. #11: Journal: Nat.Struct.Biol. / Year: 1995 Title: Mechanism of Inhibition of HIV-1 Reverse Transcriptase by Non-nucleoside Inhibitors Authors: Esnouf, R.M. / Ren, J. / Ross, C.K. / Jones, E.Y. / Stammers, D.K. / Stuart, D.I. #12: Journal: J.Mol.Biol. / Year: 1994 Title: Crystals of HIV-1 Reverse Transcriptase Diffracting to 2.2 Angstrom Resolution Authors: Stammers, D.K. / Somers, D.O. / Ross, C.K. / Kirby, I. / Ray, P.H. / Wilson, J.E. / Norman, M. / Ren, J. / Esnouf, R.M. / Garman, E. / Jones, E.Y. / Stuart, D.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ep4.cif.gz | 201.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ep4.ent.gz | 167 KB | Display | PDB format |
PDBx/mmJSON format | 1ep4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ep/1ep4 ftp://data.pdbj.org/pub/pdb/validation_reports/ep/1ep4 | HTTPS FTP |
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-Related structure data
Related structure data | |
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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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Details | HIV-1 RT is a heterodimer consisting of a p66 and a p51 subunits, the p51 contains the first 440 residues of the p66. |
-Components
#1: Protein | Mass: 64594.949 Da / Num. of mol.: 1 / Fragment: P66 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: HXB2 / Plasmid: PKK233-2 / Production host: Escherichia coli (E. coli) / References: UniProt: P04585, RNA-directed DNA polymerase |
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#2: Protein | Mass: 51399.047 Da / Num. of mol.: 1 / Fragment: P51 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: HXB2 / Plasmid: PKK233-2 / Production host: Escherichia coli (E. coli) / References: UniProt: P04585, RNA-directed DNA polymerase |
#3: Chemical | ChemComp-S11 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.01 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5 Details: see reference 12, pH 5, VAPOR DIFFUSION, SITTING DROP, temperature 277K | |||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 56 % | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 6, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. obs: 35008 / % possible obs: 90.9 % / Observed criterion σ(I): -1.5 / Redundancy: 3.1 % / Biso Wilson estimate: 62.9 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.16 / Num. unique all: 3261 / % possible all: 86.2 |
Reflection | *PLUS Num. measured all: 108379 |
Reflection shell | *PLUS % possible obs: 86.2 % |
-Processing
Software |
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Refinement | Resolution: 2.5→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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