1F84 | pdb_00001f84

SOLUTION STRUCTURE OF HCV IRES RNA DOMAIN IIID

• PDB DOI: https://doi.org/10.2210/pdb1F84/pdb
• NAKB: 1F84

• Classification: RNA
• Mutation(s): No 


• Deposited: 2000-06-28 Released: 2000-11-17 
• Deposition Author(s): Lukavsky, P.J., Otto, G.A., Lancaster, A.M., Sarnow, P., Puglisi, J.D.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 25 
• Selection Criteria: structures with the least restraint violations,structures with the lowest energy 

Literature

Structures of two RNA domains essential for hepatitis C virus internal ribosome entry site function.

Lukavsky, P.J., Otto, G.A., Lancaster, A.M., Sarnow, P., Puglisi, J.D.

(2000) Nat Struct Biol 7: 1105-1110

• PubMed: 11101890 
• DOI: https://doi.org/10.1038/81951
• Primary Citation of Related Structures:  
  1F84, 1F85


• PubMed Abstract: 
  

  Translation of the hepatitis C virus (HCV) polyprotein is initiated at an internal ribosome entry site (IRES) element in the 5' untranslated region of HCV RNA. The HCV IRES element interacts directly with the 40S subunit, and biochemical experiments have implicated RNA elements near the AUG start codon as required for IRES-40S subunit complex formation. The data we present here show that two RNA stem loops, domains IIId and IIIe, are involved in IRES-40S subunit interaction. The structures of the two RNA domains were solved by NMR spectroscopy and reveal structural features that may explain their role in IRES function.

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Organizational Affiliation: 

Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305-5126, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 9.45 kDa 
• Atom Count: 626 
• Modeled Residue Count: 29 
• Deposited Residue Count: 29 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
HCV-1B IRES RNA DOMAIN IIID	A	29	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 25 
• Selection Criteria: structures with the least restraint violations,structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-11-17 
Deposition Author(s): Lukavsky, P.J., Otto, G.A., Lancaster, A.M., Sarnow, P., Puglisi, J.D.

Revision History  

• Version 1.0: 2000-11-17
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-02-23
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-05-22
  Changes: Data collection