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Yorodumi- PDB-1qe1: CRYSTAL STRUCTURE OF 3TC-RESISTANT M184I MUTANT OF HIV-1 REVERSE ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qe1 | ||||||
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Title | CRYSTAL STRUCTURE OF 3TC-RESISTANT M184I MUTANT OF HIV-1 REVERSE TRANSCRIPTASE | ||||||
Components |
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Keywords | TRANSFERASE / HIV / REVERSE TRANSCRIPTASE / 3TC / RESISTANCE / MUTANT / DNA POLYMERASE | ||||||
Function / homology | Function and homology information HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / 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 / 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 / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus type 1 BH10 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.85 Å | ||||||
Authors | Sarafianos, S.G. / Das, K. / Ding, J. / Hughes, S.H. / Arnold, E. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1999 Title: Lamivudine (3TC) resistance in HIV-1 reverse transcriptase involves steric hindrance with beta-branched amino acids. Authors: Sarafianos, S.G. / Das, K. / Clark Jr., A.D. / Ding, J. / Boyer, P.L. / Hughes, S.H. / Arnold, E. #1: Journal: Structure / Year: 1996 Title: Structure of Unliganded HIV-1 Reverse Transcriptase at 2.7 A resolution: Implications of conformational changes for polymerization and inhibition mechanisms Authors: Hsiou, Y. / Ding, J. / Das, K. / Clark Jr., A.D. / Hughes, S.H. / Arnold, E. #2: Journal: J.Mol.Biol. / Year: 1998 Title: Structure and Functional Implications of the Polymerase Active Site Region in a Complex of HIV-1 RT with a Double-Stranded DNA and an Antibody Fab Fragment at 2.8 Angstroms Resolution Authors: Ding, J. / Das, K. / Hsiou, Y. / Sarafianos, S.G. / Clark Jr., A.D. / Jacobo-Molina, A. / Tantillo, C. / Hughes, S.H. / Arnold, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qe1.cif.gz | 199.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qe1.ent.gz | 160.7 KB | Display | PDB format |
PDBx/mmJSON format | 1qe1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qe/1qe1 ftp://data.pdbj.org/pub/pdb/validation_reports/qe/1qe1 | 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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Details | Heterodimer, of two subunits, P66 and P51. P51 contains the N-terminal 440 residues of the P66 subunit. |
-Components
#1: Protein | Mass: 64256.613 Da / Num. of mol.: 1 / Fragment: SUBUNIT A (P66), RESIDUES 168-725 / Mutation: M184I,C280S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 BH10 Genus: Lentivirus / Species: Human immunodeficiency virus 1Subtypes of HIV / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, RNA-directed DNA polymerase |
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#2: Protein | Mass: 49893.320 Da / Num. of mol.: 1 / Fragment: SUBUNIT B (P51), RESIDUES 168-594 / Mutation: M184I,C280S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 BH10 Genus: Lentivirus / Species: Human immunodeficiency virus 1Subtypes of HIV / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, RNA-directed DNA polymerase |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.48 Å3/Da / Density % sol: 64.7 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: PEG 8000, GLYCEROL, BIS-TRIS, AMMONIUM SULFATE, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 108 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.928 |
Detector | Type: PRINCETON 2K / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.928 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→40 Å / Num. all: 37000 / Num. obs: 35177 / % possible obs: 95 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.09 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 2.85→2.95 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.36 / % possible all: 88 |
Reflection | *PLUS Lowest resolution: 40 Å / % possible obs: 95 % / Rmerge(I) obs: 0.09 |
Reflection shell | *PLUS % possible obs: 88 % |
-Processing
Software |
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Refinement | Resolution: 2.85→8 Å / Cross valid method: THROUGHOUT / σ(I): 1 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.85→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 8 Å / Rfactor obs: 0.259 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |