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Yorodumi- PDB-1rti: HIGH RESOLUTION STRUCTURES OF HIV-1 RT FROM FOUR RT-INHIBITOR COM... -
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-Basic information
Entry | Database: PDB / ID: 1rti | ||||||
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Title | HIGH RESOLUTION STRUCTURES OF HIV-1 RT FROM FOUR RT-INHIBITOR COMPLEXES | ||||||
Components | (HIV-1 REVERSE TRANSCRIPTASEReverse transcriptase) x 2 | ||||||
Keywords | NUCLEOTIDYLTRANSFERASE / HIV-1 REVERSE TRANSCRIPTASE | ||||||
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 / 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 / Uncoating of the HIV Virion / 2-LTR circle formation / 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 / Assembly Of The HIV Virion / HIV-1 retropepsin / : / Budding and maturation of HIV virion / retroviral ribonuclease H / 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 / Resolution: 3 Å | ||||||
Authors | Ren, J. / Esnouf, R. / Garman, E. / Somers, D. / Ross, C. / Kirby, I. / Keeling, J. / Darby, G. / Jones, Y. / Stuart, D. / Stammers, D. | ||||||
Citation | 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. #1: 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. #2: 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. / 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 | 1rti.cif.gz | 200 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rti.ent.gz | 166.5 KB | Display | PDB format |
PDBx/mmJSON format | 1rti.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rt/1rti ftp://data.pdbj.org/pub/pdb/validation_reports/rt/1rti | 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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Atom site foot note | 1: CIS PROLINE - PRO A 226 / 2: CIS PROLINE - PRO A 421 |
-Components
#1: Protein | Mass: 64594.949 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: HXB2 ISOLATE / Cell line: 293 / Gene: HIV-1 POL / Gene (production host): HIV-1 POL / Production host: Escherichia coli (E. coli) / Strain (production host): 293 / 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.) Human immunodeficiency virus 1 / Genus: Lentivirus / Cell line: 293 / Gene: HIV-1 POL / Gene (production host): HIV-1 POL / Production host: Escherichia coli (E. coli) / Strain (production host): 293 / References: UniProt: P04585, RNA-directed DNA polymerase |
#3: Chemical | ChemComp-HEF / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.05 % | |||||||||||||||
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Crystal | *PLUS Density % sol: 50 % | |||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 5 / Method: vapor diffusion, sitting drop | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.882 Å | |||||||||
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Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: May 5, 1994 | |||||||||
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 3→25 Å / Num. obs: 20390 / % possible obs: 86.3 % / Redundancy: 8.04 % / Rmerge(I) obs: 0.123 | |||||||||
Reflection | *PLUS Num. measured all: 163954 / Rmerge(I) obs: 0.123 |
-Processing
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Refinement | Resolution: 3→25 Å / σ(F): 0 Details: DUE TO THE LOWER RESOLUTION OF THE DATA, ATOMS DISTANT FROM THE NNI-BINDING SITE (DEFINED AS ATOMS MORE THAN 20 ANGSTROMS FROM THE CA ATOM OF TYR 188) WERE TIGHTLY RESTRAINED TO THEIR ...Details: DUE TO THE LOWER RESOLUTION OF THE DATA, ATOMS DISTANT FROM THE NNI-BINDING SITE (DEFINED AS ATOMS MORE THAN 20 ANGSTROMS FROM THE CA ATOM OF TYR 188) WERE TIGHTLY RESTRAINED TO THEIR POSITION IN THE STRUCTURE OF RT AND 1051U91 COMPLEX, AND STRONG STEREOCHEMICAL RESTRAINTS WERE EMPLOYED IN THE REFINEMENT.
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Displacement parameters | Biso mean: 62 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→25 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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