Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 12.44 kDa 
• Atom Count: 823 
• Modelled Residue Count: 38 
• Deposited Residue Count: 38 
• Unique nucleic acid chains: 1

2KTZ

Inhibitor Induced Structural Change in the HCV IRES Domain IIa RNA

• PDB DOI: 10.2210/pdb2KTZ/pdb
• NDB: 2KTZ

• Classification: RNA
• Organism(s): Hepacivirus C
• Mutation(s): No 


• Deposited: 2010-02-10 Released: 2010-04-28 
• Deposition Author(s): Paulsen, R.B., Seth, P.P., Swayze, E.E., Griffey, R.H., Skalicky, J.J., Cheatham III, T.E., Davis, D.R.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 16 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

Inhibitor-induced structural change in the HCV IRES domain IIa RNA.

Paulsen, R.B., Seth, P.P., Swayze, E.E., Griffey, R.H., Skalicky, J.J., Cheatham, T.E., Davis, D.R.

(2010) Proc Natl Acad Sci U S A 107: 7263-7268

• PubMed: 20360559 
• DOI: 10.1073/pnas.0911896107
• Primary Citation of Related Structures:  
  2KTZ, 2KU0


• PubMed Abstract: 
  

Translation of the hepatitis C virus (HCV) RNA is initiated from a highly structured internal ribosomal entry site (IRES) in the 5' untranslated region (5' UTR) of the RNA genome. An important structural feature of the native RNA is an approximately 90 degrees helical bend localized to domain IIa that positions the apical loop of domain IIb of the IRES near the 40S ribosomal E-site to promote eIF2-GDP release, facilitating 80S ribosome assembly. We report here the NMR structure of a domain IIa construct in complex with a potent small-molecule inhibitor of HCV replication. Molecular dynamics refinement in explicit solvent and subsequent energetic analysis indicated that each inhibitor stereoisomer bound with comparable affinity and in an equivalent binding mode. The in silico analysis was substantiated by fluorescence-based assays showing that the relative binding free energies differed by only 0.7 kcal/mol. Binding of the inhibitor displaces key nucleotide residues within the bulge region, effecting a major conformational change that eliminates the bent RNA helical trajectory, providing a mechanism for the antiviral activity of this inhibitor class.

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Organizational Affiliation: 

Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
HCV IRES Domain IIa RNA	A	38	Hepacivirus C

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ISH	B [auth A]	(7R)-7-[(dimethylamino)methyl]-1-[3-(dimethylamino)propyl]-7,8-dihydro-1H-furo[3,2-e]benzimidazol-2-amine C17 H27 N5 O PFHMRNGLRJXGSW-GFCCVEGCSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
ISH	PDBBind:  2KTZ	Kd: 9000 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 16 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 2KTZ Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-02-10 
• Released Date: 2010-04-28 
Deposition Author(s): Paulsen, R.B., Seth, P.P., Swayze, E.E., Griffey, R.H., Skalicky, J.J., Cheatham III, T.E., Davis, D.R.

Revision History  

• Version 1.0: 2010-04-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2022-03-16
  Changes: Data collection, Database references, Derived calculations