1RFR

NMR structure of the 30mer stemloop-D of coxsackieviral RNA

• PDB DOI: https://doi.org/10.2210/pdb1RFR/pdb
• BMRB: 6042
• NAKB: 1RFR

• Classification: RNA
• Organism(s): Coxsackievirus B3
• Mutation(s): No 


• Deposited: 2003-11-10 Released: 2004-03-23 
• Deposition Author(s): Ohlenschlager, O., Wohnert, J., Bucci, E., Seitz, S., Hafner, S., Ramachandran, R., Zell, R., Gorlach, M.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy,target function 

Literature

The structure of the stemloop D subdomain of coxsackievirus B3 cloverleaf RNA and its interaction with the proteinase 3C.

Ohlenschlager, O., Wohnert, J., Bucci, E., Seitz, S., Hafner, S., Ramachandran, R., Zell, R., Gorlach, M.

(2004) Structure 12: 237-248

• PubMed: 14962384 
• DOI: https://doi.org/10.1016/j.str.2004.01.014
• Primary Citation of Related Structures:  
  1RFR


• PubMed Abstract: 
  

  Stemloop D (SLD) of the 5' cloverleaf RNA is the cognate ligand of the coxsackievirus B3 (CVB3) 3C proteinase (3Cpro). Both are indispensable components of the viral replication initiation complex. SLD is a structurally autonomous subunit of the 5' cloverleaf. The SLD structure was solved by NMR spectroscopy to an rms deviation of 0.66 A (all heavy atoms). SLD contains a novel triple pyrimidine mismatch motif with a central Watson-Crick type C:U pair. SLD is capped by an apical uCACGg tetraloop adopting a structure highly similar to stable cUNCGg tetraloops. Binding of CVB3 3Cpro induces changes in NMR spectra for nucleotides adjacent to the triple pyrimidine mismatch and of the tetraloop implying them as sites of specific SLD:3Cpro interaction. The binding of 3Cpro to SLD requires the integrity of those structural elements, strongly suggesting that 3Cpro recognizes a structural motif instead of a specific sequence.

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Organizational Affiliation: 

Institut für Molekulare Biotechnologie eV, Bentenbergstr 100813, D-07745 Jena, Germany.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 9.54 kDa 
• Atom Count: 629 
• Modelled Residue Count: 30 
• Deposited Residue Count: 30 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
stemloop-D RNA of the 5'-cloverleaf of coxsackievirus B3	A	30	Coxsackievirus B3

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy,target function 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-03-23 
Deposition Author(s): Ohlenschlager, O., Wohnert, J., Bucci, E., Seitz, S., Hafner, S., Ramachandran, R., Zell, R., Gorlach, M.

Revision History  

• Version 1.0: 2004-03-23
  Type: Initial release
  
• Version 1.1: 2008-04-29
  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
• Version 1.4: 2024-05-22
  Changes: Data collection