484D

SOLUTION STRUCTURE OF HIV-1 REV PEPTIDE-RNA APTAMER COMPLEX

• PDB DOI: https://doi.org/10.2210/pdb484D/pdb
• NAKB: 484D

• Classification: RNA BINDING PROTEIN/RNA
• Organism(s): Human immunodeficiency virus 1
• Mutation(s): No 


• Deposited: 1999-08-02 Released: 1999-10-14 
• Deposition Author(s): Ye, X., Gorin, A.A., Frederick, R., Hu, W., Majumdar, A., Xu, W., Mclendon, G., Ellington, A., Patel, D.J.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 60 
• Conformers Submitted: 22 
• Selection Criteria: LEAST RESTRAINT VIOLATION 

Literature

RNA architecture dictates the conformations of a bound peptide.

Ye, X., Gorin, A., Frederick, R., Hu, W., Majumdar, A., Xu, W., McLendon, G., Ellington, A., Patel, D.J.

(1999) Chem Biol 6: 657-669

• PubMed: 10467126 
• DOI: https://doi.org/10.1016/s1074-5521(99)80117-3
• Primary Citation of Related Structures:  
  484D


• PubMed Abstract: 
  

  The biological function of several viral and bacteriophage proteins, and their arginine-rich subdomains, involves RNA-mediated interactions. It has been shown recently that bound peptides adopt either beta-hairpin or alpha-helical conformations in viral and phage peptide-RNA complexes. We have compared the structures of the arginine-rich peptide domain of HIV-1 Rev bound to two RNA aptamers to determine whether RNA architecture can dictate the conformations of a bound peptide.

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Organizational Affiliation: 

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

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 11.15 kDa 
• Atom Count: 747 
• Modelled Residue Count: 44 
• Deposited Residue Count: 44 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BASIC REV PEPTIDE	B [auth A]	17	N/A	Mutation(s): 0
UniProt
Find proteins for Q79994 (Human immunodeficiency virus 1) Explore Q79994  Go to UniProtKB:  Q79994

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA APTAMER	A [auth B]	27	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 60 
• Conformers Submitted: 22 
• Selection Criteria: LEAST RESTRAINT VIOLATION 

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-10-14 
Deposition Author(s): Ye, X., Gorin, A.A., Frederick, R., Hu, W., Majumdar, A., Xu, W., Mclendon, G., Ellington, A., Patel, D.J.

Revision History  

• Version 1.0: 1999-10-14
  Type: Initial release
  
• Version 1.1: 2007-10-21
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-03-16
  Changes: Database references, Derived calculations
• Version 1.4: 2023-12-27
  Changes: Data collection