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Yorodumi- PDB-1ncp: STRUCTURAL CHARACTERIZATION OF A 39 RESIDUE SYNTHETIC PEPTIDE CON... -
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Entry | Database: PDB / ID: 1ncp | ||||||
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Title | STRUCTURAL CHARACTERIZATION OF A 39 RESIDUE SYNTHETIC PEPTIDE CONTAINING THE TWO ZINC BINDING DOMAINS FROM THE HIV-1 P7 NUCLEOCAPSID PROTEIN BY CD AND NMR SPECTROSCOPY | ||||||
Components | (HIV-1 P7 NUCLEOCAPSID PROTEIN) x 2 | ||||||
Keywords | VIRAL PROTEIN / NUCLEOCAPSID PROTEIN | ||||||
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 / 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 / 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 / proteolysis / DNA binding / zinc ion binding / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | SOLUTION NMR | ||||||
Authors | Clore, G.M. / Omichinski, J.G. / Gronenborn, A.M. | ||||||
Citation | Journal: FEBS Lett. / Year: 1991 Title: Structural characterization of a 39-residue synthetic peptide containing the two zinc binding domains from the HIV-1 p7 nucleocapsid protein by CD and NMR spectroscopy. Authors: Omichinski, J.G. / Clore, G.M. / Sakaguchi, K. / Appella, E. / Gronenborn, A.M. | ||||||
History |
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-Structure visualization
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PDBx/mmCIF format | 1ncp.cif.gz | 29.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ncp.ent.gz | 13.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ncp.json.gz | Tree view | PDBx/mmJSON format | |
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Summary document | 1ncp_validation.pdf.gz | 347.2 KB | Display | wwPDB validaton report |
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Full document | 1ncp_full_validation.pdf.gz | 349.5 KB | Display | |
Data in XML | 1ncp_validation.xml.gz | 2.8 KB | Display | |
Data in CIF | 1ncp_validation.cif.gz | 3.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nc/1ncp ftp://data.pdbj.org/pub/pdb/validation_reports/nc/1ncp | HTTPS FTP |
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Similar structure data |
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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: 1928.247 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / References: UniProt: P04585 |
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#2: Protein/peptide | Mass: 2073.419 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / References: UniProt: P24740 |
#3: Chemical |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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-Processing
Refinement | Software ordinal: 1 Details: THIS ENTRY CONTAINS SOLUTION NMR STRUCTURE OF A 39 RESIDUE SYNTHETIC PEPTIDE CONTAINING THE TWO ZINC BINDING DOMAINS FROM THE HIV-1 P7 NUCLEOCAPSID PROTEIN. THE TWO DOMAINS ARE COMPLETELY ...Details: THIS ENTRY CONTAINS SOLUTION NMR STRUCTURE OF A 39 RESIDUE SYNTHETIC PEPTIDE CONTAINING THE TWO ZINC BINDING DOMAINS FROM THE HIV-1 P7 NUCLEOCAPSID PROTEIN. THE TWO DOMAINS ARE COMPLETELY INDEPENDENT AND WERE SOLVED SEPARATELY. THE FIRST DOMAIN (CHAIN *N*, RESIDUES 1 - 17) WAS BASED ON 147 APPROXIMATE INTERPROTON DISTANCE RESTRAINTS. THE SECOND DOMAIN (CHAIN *C*, RESIDUES 22 - 39) WAS BASED ON 148 APPROXIMATE INTERPROTON DISTANCE RESTRAINTS. THE LINKER REGION IS HIGHLY FLEXIBLE AND CANNOT BE DEFINED FROM THE NMR DATA. THE METHOD USED TO DETERMINE THE STRUCTURES IS THE HYBRID METRIC MATRIX DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING METHOD (NILGES, CLORE, AND GRONENBORN, FEBS LETT. 229, 317 (1988)). A TOTAL OF 15 SIMULATED ANNEALING STRUCTURES WAS CALCULATED FOR EACH DOMAIN. THE COORDINATES OF THE DOMAINS WERE THEN AVERAGED AND SUBJECTED TO RESTRAINED REGULARIZATION TO YIELD THE RESTRAINED MINIMIZED STRUCTURES. ONLY THESE COORDINATES ARE LISTED. THE FIRST CHAIN IS THE N-TERMINAL DOMAIN, AND THE SECOND IS THE C-TERMINAL DOMAIN. THE FIELD PRESENTED IN COLUMNS 61 - 66 IN THIS COORDINATE FILE REPRESENTS THE ATOMIC RMS DEVIATION OF THE INDIVIDUAL STRUCTURES ABOUT THE MEAN COORDINATE POSITIONS FOR EACH DOMAIN. THE COORDINATES OF THE TWO DOMAINS HAVE BEEN BEST FITTED TO EACH OTHER. |
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NMR ensemble | Conformers submitted total number: 1 |