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Yorodumi- PDB-1lwc: CRYSTAL STRUCTURE OF M184V MUTANT HIV-1 REVERSE TRANSCRIPTASE IN ... -
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Entry | Database: PDB / ID: 1lwc | ||||||
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Title | CRYSTAL STRUCTURE OF M184V MUTANT HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX WITH NEVIRAPINE | ||||||
Components | (HIV-1 REVERSE TRANSCRIPTASE) x 2 | ||||||
Keywords | TRANSFERASE / HIV-1 REVERSE TRANSCRIPTASE / AIDS / AZT / 3TC / NRTI / NEVIRAPINE / DRUG RESISTANCE MUTATIONS | ||||||
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 / aspartic-type endopeptidase activity / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / 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 / MOLECULAR REPLACEMENT / Resolution: 2.62 Å | ||||||
Authors | Ren, J. / Chamberlain, P.P. / Nichols, C.E. / Douglas, L. / Stuart, D.I. / Stammers, D.K. | ||||||
Citation | Journal: J.Virol. / Year: 2002 Title: Crystal structures of Zidovudine- or Lamivudine-resistant human immunodeficiency virus type 1 reverse transcriptases containing mutations at codons 41, 184, and 215. Authors: Chamberlain, P.P. / Ren, J. / Nichols, C.E. / Douglas, L. / Lennerstrand, J. / Larder, B.A. / Stuart, D.I. / Stammers, D.K. #1: Journal: J.Mol.Biol. / Year: 2001 Title: Structural Mechanisms of Drug Resistance for Mutations at Codons 181 and 188 in HIV-1 Reverse Transcriptase and the Improved Resilience of Second Generation Non-Nucleoside Inhibitors Authors: Ren, J. / Nichols, C.E. / Bird, L.E. / Chamberlain, P. / Weaver, K.L. / Short, S.A. / Stuart, D.I. / Stammers, D.K. #2: Journal: J.Med.Chem. / Year: 2001 Title: 2-Amino-6-Arylsulfonylbenzonitriles as Non-Nucleoside reverse Transcriptase Inhibitors of HIV-1 Authors: Chan, J.H. / Hong, J.S. / Hunter III, R.N. / Orr, G.F. / Cowan, J.R. / Sherman, D.B. / Sparks, S.M. / Reitter, B.E. / Andrews III, C.W. / Hazen, R.J. / St Clair, M. / Boone, L.R. / Ferris, R. ...Authors: Chan, J.H. / Hong, J.S. / Hunter III, R.N. / Orr, G.F. / Cowan, J.R. / Sherman, D.B. / Sparks, S.M. / Reitter, B.E. / Andrews III, C.W. / Hazen, R.J. / St Clair, M. / Boone, L.R. / Ferris, R.G. / Creech, K.L. / Roberts, G.B. / Short, S.A. / Weaver, K.L. / Ott, R.J. / Ren, J. / Hopkins, A.L. / Stuart, D.I. / Stammers, D.K. #3: Journal: Structure / Year: 2000 Title: Structural Basis for the Resilience of Efavirenz (Dmp-266) to Drug Resistance Mutations in HIV-1 Reverse Transcriptase Authors: Ren, J. / Milton, J. / Weaver, K.L. / Short, S.A. / Stuart, D.I. / Stammers, D.K. #4: 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.E. / Bird, L.E. / Fujiwara, T. / Sugimoto, H. / Stuart, D.I. / Stammers, D.K. #5: 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. #6: Journal: J.Med.Chem. / Year: 1999 Title: Crystallographic Analysis of the Binding Modes of Thiazoloisoindolinone Non-Nucleoside 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. #7: 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. #8: 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. #9: 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. #10: 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. #11: 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. #12: 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.K. / Miyasaka, T. / Walker, R.T. / Tanaka, H. / Stammers, D.K. / Stuart, D.I. #13: 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. / Stammers, D.K. / Stuart, D.I. #14: 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. #15: 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. #16: 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. / 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 | 1lwc.cif.gz | 197.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lwc.ent.gz | 163.7 KB | Display | PDB format |
PDBx/mmJSON format | 1lwc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lwc_validation.pdf.gz | 785.4 KB | Display | wwPDB validaton report |
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Full document | 1lwc_full_validation.pdf.gz | 827.9 KB | Display | |
Data in XML | 1lwc_validation.xml.gz | 37.1 KB | Display | |
Data in CIF | 1lwc_validation.cif.gz | 50.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lw/1lwc ftp://data.pdbj.org/pub/pdb/validation_reports/lw/1lwc | HTTPS FTP |
-Related 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: 64562.887 Da / Num. of mol.: 1 / Fragment: p66 / Mutation: M184V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: HIV-1 POL / Plasmid: pkk233-2 / Production host: Escherichia coli (E. coli) / Strain (production host): TG-1 / References: UniProt: P04585, RNA-directed DNA polymerase | ||||
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#2: Protein | Mass: 51366.984 Da / Num. of mol.: 1 / Fragment: p51 / Mutation: M184V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: HIV-1 POL / Plasmid: pkk233-2 / Production host: Escherichia coli (E. coli) / Strain (production host): TG-1 / References: UniProt: P04585, RNA-directed DNA polymerase | ||||
#3: Chemical | #4: Chemical | ChemComp-NVP / | #5: 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: 2.27 Å3/Da / Density % sol: 45.81 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5 Details: pH 5.00, VAPOR DIFFUSION, SITTING DROP, temperature 277K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 5 / Details: Stammers, D.K., (1994) J.Mol.Biol., 242, 586. | |||||||||||||||||||||||||
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: ESRF / Beamline: ID2 / Wavelength: 0.9903 / Wavelength: 0.9903 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 27, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9903 Å / Relative weight: 1 |
Reflection | Resolution: 2.62→30 Å / Num. obs: 28631 / % possible obs: 86.8 % / Observed criterion σ(I): -1.5 / Redundancy: 4.7 % / Biso Wilson estimate: 68.1 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 2.62→2.71 Å / Mean I/σ(I) obs: 2 / % possible all: 71.6 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 134485 / Rmerge(I) obs: 0.075 |
Reflection shell | *PLUS % possible obs: 71.6 % / Num. unique obs: 2326 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.62→29.8 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2144345.6 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.9638 Å2 / ksol: 0.329074 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 77.2 Å2
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Refine analyze | Luzzati coordinate error free: 0.45 Å / Luzzati sigma a free: 0.45 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.62→29.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.62→2.71 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Lowest resolution: 30 Å / Rfactor obs: 0.207 / Rfactor Rfree: 0.28 / Rfactor Rwork: 0.214 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.388 / Rfactor Rwork: 0.314 |