[English] 日本語
Yorodumi- PDB-1rt3: AZT DRUG RESISTANT HIV-1 REVERSE TRANSCRIPTASE COMPLEXED WITH 1051U91 -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rt3 | ||||||
---|---|---|---|---|---|---|---|
Title | AZT DRUG RESISTANT HIV-1 REVERSE TRANSCRIPTASE COMPLEXED WITH 1051U91 | ||||||
Components | (HIV-1 REVERSE TRANSCRIPTASEReverse transcriptase) x 2 | ||||||
Keywords | NUCLEOTIDYLTRANSFERASE / HIV-1 REVERSE TRANSCRIPTASE / AIDS / NUCLEOSIDE INHIBITOR / DRUG RESISTANCE MUTATION | ||||||
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 / Uncoating of the HIV Virion / 2-LTR circle formation / Early Phase of HIV Life Cycle / Vpr-mediated nuclear import of PICs / 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 / Uncoating of the HIV Virion / 2-LTR circle formation / Early Phase of HIV Life Cycle / Vpr-mediated nuclear import of PICs / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / viral life cycle / Assembly Of The HIV Virion / HIV-1 retropepsin / : / retroviral ribonuclease H / Budding and maturation of HIV virion / exoribonuclease H / : / exoribonuclease H activity / protein processing / host multivesicular body / 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 / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / peptidase activity / 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 / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / DNA binding / RNA binding / zinc ion binding / membrane / identical protein binding Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Ren, J. / Stammers, D.K. / Stuart, D.I. | ||||||
Citation | 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. #1: 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. #2: 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. #3: 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. #4: 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. #5: 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. #6: 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1rt3.cif.gz | 195.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1rt3.ent.gz | 159.2 KB | Display | PDB format |
PDBx/mmJSON format | 1rt3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rt/1rt3 ftp://data.pdbj.org/pub/pdb/validation_reports/rt/1rt3 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1revS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 64666.996 Da / Num. of mol.: 1 / Mutation: D67N, K70R, T215F, K219Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Cell line: 293 / Gene: POL / Variant: HXB2 ISOLATE / Production host: Escherichia coli (E. coli) / Strain (production host): 293 / References: UniProt: P04585, RNA-directed DNA polymerase |
---|---|
#2: Protein | Mass: 51426.074 Da / Num. of mol.: 1 / Mutation: D67N, K70R, T215F, K219Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Cell line: 293 / Gene: POL / Variant: HXB2 ISOLATE / Production host: Escherichia coli (E. coli) / Strain (production host): 293 / References: UniProt: P04585, RNA-directed DNA polymerase |
#3: Chemical | ChemComp-U05 / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 44.8 % | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 5 / Details: pH 5.0 | |||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 56 % | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, sitting dropDetails: drop solution was mixed with an equal volume of reservoir solution | |||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: May 1, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→25 Å / Num. obs: 17935 / % possible obs: 83.3 % / Observed criterion σ(I): 0 / Redundancy: 2.36 % / Rmerge(I) obs: 0.132 / Net I/σ(I): 6.01 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 1.71 % / Rmerge(I) obs: 0.531 / Mean I/σ(I) obs: 1.29 / % possible all: 64.2 |
Reflection | *PLUS Num. measured all: 42414 |
Reflection shell | *PLUS % possible obs: 64.2 % / Num. unique obs: 1375 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: RT-9-CL-TIBO COMPLEX, PDB ENTRY 1REV Resolution: 3→25 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 20 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 20 ANGSTROM FROM THE CA ATOM OF TYR188) WERE TIGHTLY RESTRAINED TO THEIR POSITION IN THE NINE-DOMAIN RIGID-BODY REFINED MODEL OF RT-9-CL-TIBO 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 0.222.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→25 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3→3.14 Å / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor obs: 0.416 |