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Yorodumi- PDB-1wje: SOLUTION STRUCTURE OF H12C MUTANT OF THE N-TERMINAL ZN BINDING DO... -
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Entry | Database: PDB / ID: 1wje | ||||||
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Title | SOLUTION STRUCTURE OF H12C MUTANT OF THE N-TERMINAL ZN BINDING DOMAIN OF HIV-1 INTEGRASE COMPLEXED TO CADMIUM, NMR, MINIMIZED AVERAGE STRUCTURE | ||||||
Components | HIV-1 INTEGRASE | ||||||
Keywords | ZN-BINDING PROTEIN / AIDS / POLYPROTEIN / HYDROLASE / ASPARTYL PROTEASE | ||||||
Function / homology | Function and homology information HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus ...HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / 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 / 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 / proteolysis / DNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Cai, M. / Gronenborn, A.M. / Clore, G.M. | ||||||
Citation | Journal: Protein Sci. / Year: 1998 Title: Solution structure of the His12 --> Cys mutant of the N-terminal zinc binding domain of HIV-1 integrase complexed to cadmium. Authors: Cai, M. / Huang, Y. / Caffrey, M. / Zheng, R. / Craigie, R. / Clore, G.M. / Gronenborn, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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PDBx/mmCIF format | 1wje.cif.gz | 43.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wje.ent.gz | 30.7 KB | Display | PDB format |
PDBx/mmJSON format | 1wje.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1wje_validation.pdf.gz | 337 KB | Display | wwPDB validaton report |
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Full document | 1wje_full_validation.pdf.gz | 338.6 KB | Display | |
Data in XML | 1wje_validation.xml.gz | 3 KB | Display | |
Data in CIF | 1wje_validation.cif.gz | 3.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wj/1wje ftp://data.pdbj.org/pub/pdb/validation_reports/wj/1wje | HTTPS FTP |
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Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 5235.964 Da / Num. of mol.: 2 / Mutation: H12C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Cell line: BL21 / Gene: POTENTIAL / Plasmid: PET-15B / Species (production host): Escherichia coli / Gene (production host): T7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P04587 #2: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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-Sample preparation
Sample conditions | pH: 4.5 / Temperature: 308 K |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
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-Processing
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: THE STRUCTURES WERE CALCULATED USING THE SIMULATED ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT. 229, 129-136, USING THE PROGRAM XPLOR 3.1 (BRUNGER) MODIFIED TO INCORPORATE COUPLING ...Details: THE STRUCTURES WERE CALCULATED USING THE SIMULATED ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT. 229, 129-136, USING THE PROGRAM XPLOR 3.1 (BRUNGER) MODIFIED TO INCORPORATE COUPLING CONSTANT (GARRETT ET AL. (1984) J. MAGN RESON. SERIES B 104, 99-103), CARBON CHEMICAL SHIFT (KUSZEWSKI ET AL. (1995) J. MAGN. RESON. SERIES B 106, 92-96) RESTRAINTS AND A CONFORMATIONAL DATABASE POTENTIAL (KUSZEWSKI ET AL. (1996) PROTEIN SCI 5, 1067-1080 AND (1997) J. MAGN. RESON. 125, 171-177). THE 3D STRUCTURE OF THE N-TERMINAL DOMAIN OF THE H12C MUTANT OF HIV-1 INTEGRASE COMPLEXED TO CADMIUM WAS SOLVED BY MULTI-DIMENSIONAL HETERONUCLEAR-EDITED AND -FILTERED NMR IS BASED ON 757 EXPERIMENTAL RESTRAINTS (PER MONOMER): (A) INTRASUBUNIT: 203 SEQUENTIAL (|I-J|=1), 161 MEDIUM RANGE (1 < |I-J| >=5) AND 82 LONG RANGE (|I-J| >5) INTERRESIDUE, AND 5 INTRARESIDUE APPROXIMATE INTERPROTON DISTANCE RESTRAINTS; 16 DISTANCE RESTRAINTS FOR 8 HYDROGEN BONDS; 117 TORSION ANGLE (45 PHI, 35 PSI, 26 CHI1, 10 CHI2 AND 1 CHI3) RESTRAINTS; 47 THREE-BOND HN-HA COUPLING CONSTANT RESTRAINTS; 99 (50 CALPHA AND 49 CBETA) 13C SHIFT RESTRAINTS. (B) 20 INTERSUBUNIT INTERPROTON DISTANCE RESTRAINTS. (C) 7 AMBIGUOUS INTERPROTON DISTANCE RESTRAINTS THAT CAN ARISE FROM INTRA AND/OR INTERSUBUNIT INTERACTIONS. THE STRUCTURES WERE CALCULATED USING THE SIMULATED ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT. 229, 129-136, USING THE PROGRAM XPLOR 3.1 (BRUNGER) MODIFIED TO INCORPORATE COUPLING CONSTANT (GARRETT ET AL. (1984) J. MAGN RESON. SERIES B 104, 99-103), CARBON CHEMICAL SHIFT (KUSZEWSKI ET AL. (1995) J. MAGN. RESON. SERIES B 106, 92-96) RESTRAINTS AND A CONFORMATIONAL DATABASE POTENTIAL (KUSZEWSKI ET AL. (1996) PROTEIN SCI 5, 1067-1080 AND (1997) J. MAGN. RESON. 125, 171-177). THE 3D STRUCTURE OF THE N-TERMINAL DOMAIN OF THE H12C MUTANT OF HIV-1 INTEGRASE COMPLEXED TO CADMIUM WAS SOLVED BY MULTI-DIMENSIONAL HETERONUCLEAR-EDITED AND -FILTERED NMR IS BASED ON 757 EXPERIMENTAL RESTRAINTS (PER MONOMER): (A) INTRASUBUNIT: 203 SEQUENTIAL (|I-J|=1), 161 MEDIUM RANGE (1 < |I-J| >=5) AND 82 LONG RANGE (|I-J| >5) INTERRESIDUE, AND 5 INTRARESIDUE APPROXIMATE INTERPROTON DISTANCE RESTRAINTS; 16 DISTANCE RESTRAINTS FOR 8 HYDROGEN BONDS; 117 TORSION ANGLE (45 PHI, 35 PSI, 26 CHI1, 10 CHI2 AND 1 CHI3) RESTRAINTS; 47 THREE-BOND HN-HA COUPLING CONSTANT RESTRAINTS; 99 (50 CALPHA AND 49 CBETA) 13C SHIFT RESTRAINTS. (B) 20 INTERSUBUNIT INTERPROTON DISTANCE RESTRAINTS. (C) 7 AMBIGUOUS INTERPROTON DISTANCE RESTRAINTS THAT CAN ARISE FROM INTRA AND/OR INTERSUBUNIT INTERACTIONS. | ||||||||||||
NMR ensemble | Conformer selection criteria: REGULARIZED MEAN STRUCTURE / Conformers calculated total number: 40 / Conformers submitted total number: 1 |