Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 13.72 kDa 
• Atom Count: 915 
• Modelled Residue Count: 52 
• Deposited Residue Count: 52 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

1ULL

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

• PDB DOI: 10.2210/pdb1ULL/pdb
• NDB: 1ULL

• Classification: Viral protein/RNA
• Organism(s): Human immunodeficiency virus 1
• Mutation(s): No 


• Deposited: 1996-11-05 Released: 1997-08-20 
• Deposition Author(s): Ye, X., Gorin, A., Ellington, A.D., Patel, D.J.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 14 
• Conformers Submitted: 7 
• Selection Criteria: ENERGY GAP 400 KCAL/MOLE 

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

• PubMed: 8946856 
• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
REV PEPTIDE	B	17	Human immunodeficiency virus 1	Mutation(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 ID: 1
Molecule	Chains	Length	Organism	Image
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	35	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 14 
• Conformers Submitted: 7 
• Selection Criteria: ENERGY GAP 400 KCAL/MOLE 
• OLDERADO: 1ULL Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1996-11-05 
• Released Date: 1997-08-20 
Deposition Author(s): Ye, X., Gorin, A., Ellington, A.D., Patel, D.J.

Revision History  

• 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