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- PDB-1ncp: STRUCTURAL CHARACTERIZATION OF A 39 RESIDUE SYNTHETIC PEPTIDE CON... -

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Database: PDB / ID: 1ncp
TitleSTRUCTURAL 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
KeywordsVIRAL 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 / 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 / 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 / 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 / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane / identical protein binding
Similarity search - Function
Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain ...Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Gag-Pol polyprotein / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodSOLUTION NMR
AuthorsClore, G.M. / Omichinski, J.G. / Gronenborn, A.M.
CitationJournal: 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
DepositionNov 27, 1991Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 4, 2018Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
N: HIV-1 P7 NUCLEOCAPSID PROTEIN
C: HIV-1 P7 NUCLEOCAPSID PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,1324
Polymers4,0022
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representative

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Components

#1: Protein/peptide HIV-1 P7 NUCLEOCAPSID PROTEIN


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
#2: Protein/peptide HIV-1 P7 NUCLEOCAPSID PROTEIN


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 ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Processing

RefinementSoftware 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.
NMR ensembleConformers submitted total number: 1

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