1HVN

ZINC-AND SEQUENCE-DEPENDENT BINDING TO NUCLEIC ACIDS BY THE N-TERMINAL ZINC FINGER DOMAIN OF THE HIV-1 NUCLEOCAPSID PROTEIN: NMR STRUCTURE OF THE COMPLEX WITH THE PSI-SITE ANALOG, D/ACGCC


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 15 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Zinc- and sequence-dependent binding to nucleic acids by the N-terminal zinc finger of the HIV-1 nucleocapsid protein: NMR structure of the complex with the Psi-site analog, dACGCC.

South, T.L.Summers, M.F.

(1993) Protein Sci. 2: 3

  • DOI: 10.1002/pro.5560020102
  • Primary Citation of Related Structures:  1HVO

  • PubMed Abstract: 
  • The nucleic acid interactive properties of a synthetic peptide with sequence of the N-terminal CCHC zinc finger (CCHC = Cys-X2-Cys-X4-His-X4-Cys; X = variable amino acid) of the human immunodeficiency virus (HIV) nucleocapsid protein, Zn(HIV1-F1), ha ...

    The nucleic acid interactive properties of a synthetic peptide with sequence of the N-terminal CCHC zinc finger (CCHC = Cys-X2-Cys-X4-His-X4-Cys; X = variable amino acid) of the human immunodeficiency virus (HIV) nucleocapsid protein, Zn(HIV1-F1), have been studied by 1H NMR spectroscopy. Titration of Zn(HIV1-F1) with oligodeoxyribonucleic acids containing different nucleotide sequences reveals, for the first time, sequence-dependent binding that requires the presence of at least one guanosine residue for tight complex formation. The dynamics of complex formation are sensitive to the nature of the residues adjacent to guanosine, with residues on the 3' side of guanosine having the largest influence. An oligodeoxyribonucleotide with sequence corresponding to a portion of the HIV-1 psi-packaging signal, d(ACGCC), forms a relatively tight complex with Zn(HIV1-F1) (Kd = 5 x 10(-6) M). Two-dimensional nuclear Overhauser effect (NOESY) data indicate that the bound nucleic acid exists predominantly in a single-stranded, A-helical conformation, and the presence of more than a dozen intermolecular NOE cross peaks enabled three-dimensional modeling of the complex. The nucleic acid binds within a hydrophobic cleft on the peptide surface. This hydrophobic cleft is defined by the side chains of residues Val1, Phe4, Ile12, and Ala13. Backbone amide protons of Phe4 and Ala13 and the backbone carbonyl oxygen of Lys2 that lie within this cleft appear to form hydrogen bonds with the guanosine O6 and N1H atoms, respectively. In addition, the positively charged side chain of Arg14 is ideally positioned for electrostatic interactions with the phosphodiester backbone of the nucleic acid. The structural findings provide a rationalization for the general conservation of these hydrophobic and basic residues in CCHC zinc fingers, and are consistent with site-directed mutagenesis results that implicate these residues as direct participants in viral genome recognition.


    Related Citations: 
    • The C-Terminal Retroviral-Type Zinc Finger Domain from the HIV-1 Nucleocapsid Protein is Structurally Similar to the N-Terminal Zinc Finger Domain
      South, T.L.,Blake, P.R.,Hare, D.R.,Summers, M.F.
      (1991) Biochemistry 30: 6342
    • Nucleocapsid Zinc Fingers Detected in Retroviruses: Exafs Studies of Intact Viruses and the Solution-State Structure of the Nucleocapsid Protein from HIV-1
      Summers, M.F.,Henderson, L.E.,Chance, M.R.,Bess Junior, J.W.,South, T.L.,Blake, P.R.,Sagi, I.,Perez-Alvarado, G.,Sowder III, R.C.,Hare, D.R.,Arthur, L.O.
      (1992) Protein Sci. 1: 563
    • The Nucleocapsid Protein Isolated from HIV-I Particles Binds Zinc and Form Retroviral-Type Zinc Fingers
      South, T.L.,Blake, P.R.,Sowder III, R.,Arthur, L.O.,Henderson, L.E.,Summers, M.F.
      (1990) Biochemistry 29: 7786


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Maryland Baltimore County 21228.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hiv-1 Nucleocapsid Zinc Finger
E
18Human immunodeficiency virus type 1 group M subtype BGene Names: gag
Find proteins for Q70622 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  Q70622
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(P*AP*CP*GP*CP*C)-3')D5N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
E
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DNAKd: 5000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 15 
  • Olderado: 1HVN Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance