1ULL

RNA APTAMER COMPLEXED WITH HIV-1 REV PEPTIDE, NMR, 7 STRUCTURES


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 14 
  • Conformers Submitted: 
  • Selection Criteria: ENERGY GAP 400 KCAL/MOLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Deep penetration of an alpha-helix into a widened RNA major groove in the HIV-1 rev peptide-RNA aptamer complex.

Ye, X.Gorin, A.Ellington, A.D.Patel, D.J.

(1996) Nat Struct Biol 3: 1026-1033

  • DOI: 10.1038/nsb1296-1026
  • Primary Citation of Related Structures:  
    1ULL

  • PubMed Abstract: 
  • A combined NMR-molecular dynamics approach has been applied to determine the solution structure of a HIV-1 17-mer rev peptide bound to its 35-mer high affinity RNA aptamer binding site. Complex formation involves adaptive binding with the alpha-helical arginine-rich basic rev peptide targeting a widened RNA major groove centred about adjacent G ...

    A combined NMR-molecular dynamics approach has been applied to determine the solution structure of a HIV-1 17-mer rev peptide bound to its 35-mer high affinity RNA aptamer binding site. Complex formation involves adaptive binding with the alpha-helical arginine-rich basic rev peptide targeting a widened RNA major groove centred about adjacent G.A and reversed A.A mismatches. We have also identified a U AU triple in the aptamer complex with the Hoogsteen-paired uracil base sandwiched between two arginine side chains. The intermolecular contacts identified in the aptamer complex readily account for the consequences of peptide and RNA mutations, as well as the results of previous in vitro selection experiments. The details of molecular recognition associated with targeting by rev of its high affinity RNA binding sites open new opportunities for structure-based drug design strategies.


    Organizational Affiliation

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



Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
REV PEPTIDEB17Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for P05866 (Human immunodeficiency virus type 1 group M subtype B (isolate WMJ22))
Explore P05866 
Go to UniProtKB:  P05866
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05866
Protein Feature View
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
RNA (5'-R (GP*GP*CP*UP*GP*GP*AP*CP*UP*CP*GP*UP*AP*CP*UP*UP*CP*GP* GP*UP*AP*CP*UP*GP*GP*AP*GP*AP*AP*AP*CP*AP*GP*CP*C)-3')A 35N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 14 
  • Conformers Submitted: 
  • Selection Criteria: ENERGY GAP 400 KCAL/MOLE 
  • OLDERADO: 1ULL Olderado

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-08-20
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-03-02
    Changes: Database references, Derived calculations, Other