+Open data
-Basic information
Entry | Database: PDB / ID: 1rt4 | ||||||
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Title | HIV-1 REVERSE TRANSCRIPTASE COMPLEXED WITH UC781 | ||||||
Components | (HIV-1 REVERSE TRANSCRIPTASE) x 2 | ||||||
Keywords | NUCLEOTIDYLTRANSFERASE / HIV-1 REVERSE TRANSCRIPTASE / AIDS / NONNUCLEOSIDE INHIBITION / 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 / symbiont-mediated activation of host apoptosis / HIV-1 retropepsin / 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 / 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 / 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 | HIV-1 M:B_HXB2R (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Ren, J. / Stammers, D.K. / Stuart, D.I. | ||||||
Citation | Journal: Biochemistry / Year: 1998 Title: Crystal structures of HIV-1 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. #1: 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. #2: 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. #3: 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 Nonnucleoside Inhibitor Authors: Esnouf, R.M. / Ren, J. / Hopkins, A.L. / Ross, C.K. / Jones, E.Y. / Stammers, D.K. / Stuart, D.I. #4: 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: Hopkins, A.L. / Ren, J. / Esnouf, R.M. / Willcox, B.E. / Jones, E.Y. / Ross, C. / Miyasaka, T. / Walker, R.T. / Tanaka, H. / Stammers, D.K. / Stuart, D.I. #5: 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. / Hopkins, A. / Ross, C. / Jones, Y. / Stammers, D. / Stuart, D. #6: Journal: Nat.Struct.Biol. / Year: 1995 Title: High Resolution Structures of HIV-1 RT from Four RT-Inhibitor Complexes Authors: Ren, J. / Esnouf, R. / Garman, E. / Somers, D. / Ross, C. / Kirby, I. / Keeling, J. / Darby, G. / Jones, Y. / Stuart, D. / Stammers, D. #7: Journal: Nat.Struct.Biol. / Year: 1995 Title: Mechanism of Inhibition of HIV-1 Reverse Transcriptase by Non-Nucleoside Inhibitors Authors: Esnouf, R. / Ren, J. / Ross, C. / Jones, Y. / Stammers, D. / Stuart, D. #8: Journal: J.Mol.Biol. / Year: 1994 Title: Crystals of HIV-1 Reverse Transcriptase Diffracting to 2.2 A Resolution Authors: Stammers, D.K. / Somers, D.O. / Ross, C.K. / Kirby, I. / Ray, P.H. / Wilson, J.E. / Norman, M. / Ren, J.S. / Esnouf, R.M. / Garman, E.F. / 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 | 1rt4.cif.gz | 200 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rt4.ent.gz | 162.9 KB | Display | PDB format |
PDBx/mmJSON format | 1rt4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rt/1rt4 ftp://data.pdbj.org/pub/pdb/validation_reports/rt/1rt4 | HTTPS FTP |
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-Related structure data
Related structure data | 1rt5C 1rt6C 1rt7C 1rthS 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
#1: Protein | Mass: 64594.949 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HIV-1 M:B_HXB2R (virus) / Genus: Lentivirus / Species: Human immunodeficiency virus 1 / Strain: HXB2 ISOLATE / Gene: POL / 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 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HIV-1 M:B_HXB2R (virus) / Genus: Lentivirus / Species: Human immunodeficiency virus 1 / Strain: HXB2 ISOLATE / Gene: POL / Production host: Escherichia coli (E. coli) / References: UniProt: P04585, RNA-directed DNA polymerase |
#3: Chemical | ChemComp-PO4 / |
#4: Chemical | ChemComp-UC1 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50 % / Description: ALL DATA INCLUDED APART FROM OUTLIERS | ||||||||||||||||||||
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Crystal grow | pH: 5 / Details: pH 5.0 | ||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: unknown | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 289 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Apr 1, 1996 |
Radiation | Monochromator: 0.1MM / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→30 Å / Num. obs: 24503 / % possible obs: 93.6 % / Redundancy: 4.12 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 2.21 % / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 1.59 / % possible all: 62.7 |
Reflection | *PLUS Num. measured all: 101066 |
Reflection shell | *PLUS % possible obs: 62.7 % / Num. unique obs: 1545 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: RT-1051U91 COMPLEX (PDB ENTRY 1RTH) Resolution: 2.9→30 Å / Data cutoff low absF: 0 Details: DUE TO THE LOW RATIO BETWEEN THE NUMBER OF REFLECTIONS AND THE NUMBER OF PARAMETERS TO BE REFINED, ATOMS DISTANT FROM THE NNI-BINDING SITE (DEFINED AS ATOMS MORE THAN 25 ANGSTROM FROM THE CA ...Details: DUE TO THE LOW RATIO BETWEEN THE NUMBER OF REFLECTIONS AND THE NUMBER OF PARAMETERS TO BE REFINED, ATOMS DISTANT FROM THE NNI-BINDING SITE (DEFINED AS ATOMS MORE THAN 25 ANGSTROM FROM THE CA ATOM OF TYR 188) WERE TIGHTLY RESTRAINED TO THEIR POSITION IN THE NINE-DOMAIN RIGID-BODY REFINED MODEL OF RT-1051U91 COMPLEX, AND STRONG STEREOCHEMICAL RESTRAINTS WERE EMPLOYED IN THE REFINEMENT. CROSS-VALIDATION WAS ONLY USED IN THE FIRST ROUND OF REFINEMENT FROM WHICH THE ABOVE FREE R VALUES AND R VALUES ARE TAKEN. THE ABOVE THERMAL FACTOR AND RMS DEVIATIONS OF THE STEREOCHEMISTRY ARE TAKEN FROM THE FINAL MODEL WHICH WAS REFINED USING THE WHOLE DATA SET. THE FINAL R FACTOR FOR THE WHOLE DATA SET IS 0.212.
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Displacement parameters | Biso mean: 61 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.03 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.212 / Num. reflection Rfree: 1223 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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