1A1T

STRUCTURE OF THE HIV-1 NUCLEOCAPSID PROTEIN BOUND TO THE SL3 PSI-RNA RECOGNITION ELEMENT, NMR, 25 STRUCTURES


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 800 
  • Conformers Submitted: 25 
  • Selection Criteria: LEAST TOTAL PENALTY 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the HIV-1 nucleocapsid protein bound to the SL3 psi-RNA recognition element.

De Guzman, R.N.Wu, Z.R.Stalling, C.C.Pappalardo, L.Borer, P.N.Summers, M.F.

(1998) Science 279: 384-388

  • DOI: 10.1126/science.279.5349.384
  • Primary Citation of Related Structures:  
    1A1T

  • PubMed Abstract: 
  • The three-dimensional structure of the human immunodeficiency virus-type 1 (HIV-1) nucleocapsid protein (NC) bound to the SL3 stem-loop recognition element of the genomic Psi RNA packaging signal has been determined by heteronuclear magnetic resonance spectroscopy ...

    The three-dimensional structure of the human immunodeficiency virus-type 1 (HIV-1) nucleocapsid protein (NC) bound to the SL3 stem-loop recognition element of the genomic Psi RNA packaging signal has been determined by heteronuclear magnetic resonance spectroscopy. Tight binding (dissociation constant, approximately 100 nM) is mediated by specific interactions between the amino- and carboxyl-terminal CCHC-type zinc knuckles of the NC protein and the G7 and G9 nucleotide bases, respectively, of the G6-G7-A8-G9 RNA tetraloop. A8 packs against the amino-terminal knuckle and forms a hydrogen bond with conserved Arg32, and residues Lys3 to Arg10 of NC form a 310 helix that binds to the major groove of the RNA stem and also packs against the amino-terminal zinc knuckle. The structure provides insights into the mechanism of viral genome recognition, explains extensive amino acid conservation within NC, and serves as a basis for the development of inhibitors designed to interfere with genome encapsidation.


    Organizational Affiliation

    Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland-Baltimore County (UMBC), 1000 Hilltop Circle, Baltimore, MD 21250, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NUCLEOCAPSID PROTEINB [auth A]55Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: NCgag
UniProt
Find proteins for Q75677 (Human immunodeficiency virus 1)
Explore Q75677 
Go to UniProtKB:  Q75677
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    SL3 STEM-LOOP RNAA [auth B]20N/A
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ZN
    Query on ZN

    Download Ideal Coordinates CCD File 
    C [auth A], D [auth A]ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: SOLUTION NMR
    • Conformers Calculated: 800 
    • Conformers Submitted: 25 
    • Selection Criteria: LEAST TOTAL PENALTY 
    • OLDERADO: 1A1T Olderado

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 1998-06-17
      Type: Initial release
    • Version 1.1: 2008-03-03
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance