1G70

COMPLEX OF HIV-1 RRE-IIB RNA WITH RSG-1.2 PEPTIDE


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 90 
  • Conformers Submitted: 14 
  • Selection Criteria: structures with acceptable covalent geometry,structures with the least restraint violations,structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Peptide-triggered conformational switch in HIV-1 RRE RNA complexes.

Gosser, Y.Hermann, T.Majumdar, A.Hu, W.Frederick, R.Jiang, F.Xu, W.Patel, D.J.

(2001) Nat.Struct.Mol.Biol. 8: 146-150

  • DOI: 10.1038/84138

  • PubMed Abstract: 
  • We have used NMR spectroscopy to determine the solution structure of a complex between an oligonucleotide derived from stem IIB of the Rev responsive element (RRE-IIB) of HIV-1 mRNA and an in vivo selected, high affinity binding Arg-rich peptide. The ...

    We have used NMR spectroscopy to determine the solution structure of a complex between an oligonucleotide derived from stem IIB of the Rev responsive element (RRE-IIB) of HIV-1 mRNA and an in vivo selected, high affinity binding Arg-rich peptide. The peptide binds in a partially alpha-helical conformation into a pocket within the RNA deep groove. Comparison with the structure of a complex between an alpha-helical Rev peptide and RRE-IIB reveals that the sequence of the bound peptide determines the local conformation of the RRE peptide binding site. A conformational switch of an unpaired uridine base was revealed; this points out into the solvent in the Rev peptide complex, but it is stabilized inside the RNA deep groove by stacking with an Arg side chain in the selected peptide complex. The conformational switch has been visualized by NMR chemical shift mapping of the uridine H5/H6 atoms during a competition experiment in which Rev peptide was displaced from RRE-IIB by the higher affinity binding selected peptide.


    Related Citations: 
    • alpha Helix-RNA major groove recognition in an HIV-1 Rev peptide-RRE RNA complex
      Battiste, J.L.,Mao, H.,Rao, N.S.,Tan, R.,Muhandiram, D.R.,Kay, L.E.,Frankel, A.D.,Williamson, J.R.
      (1996) Science 273: 1547
    • Molding a peptide into an RNA site by in vivo peptide evolution
      Harada, K.,Martin, S.S.,Tan, R.,Frankel, A.D.
      (1997) Proc.Natl.Acad.Sci.USA 94: 11887


    Organizational Affiliation

    Cellular Biochemistry and Biophysics Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RSG-1.2 PEPTIDE
B
22N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 1
MoleculeChainsLengthOrganism
HIV-1 RRE-IIB 32 NUCLEOTIDE RNAA32Human immunodeficiency virus 1
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 90 
  • Conformers Submitted: 14 
  • Selection Criteria: structures with acceptable covalent geometry,structures with the least restraint violations,structures with the lowest energy 
  • Olderado: 1G70 Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-02-07
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance