Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 5.77 kDa 
• Atom Count: 381 
• Modelled Residue Count: 18 
• Deposited Residue Count: 18 
• Unique nucleic acid chains: 1

1Z30

NMR structure of the apical part of stemloop D from cloverleaf 1 of bovine enterovirus 1 RNA

• PDB DOI: 10.2210/pdb1Z30/pdb
• BMRB: 6562
• NDB: 1Z30

• Classification: RNA
• Mutation(s): No 


• Deposited: 2005-03-10 Released: 2005-04-26 
• Deposition Author(s): Ihle, Y., Ohlenschlager, O., Duchardt, E., Ramachandran, R., Gorlach, M.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 15 
• Selection Criteria: structures with the lowest energy, target function 

Literature

A novel cGUUAg tetraloop structure with a conserved yYNMGg-type backbone conformation from cloverleaf 1 of bovine enterovirus 1 RNA

Ihle, Y., Ohlenschlager, O., Hafner, S., Duchardt, E., Zacharias, M., Seitz, S., Zell, R., Ramachandran, R., Gorlach, M.

(2005) Nucleic Acids Res 33: 2003-2011

• PubMed: 15814817 
• DOI: 10.1093/nar/gki501
• Primary Citation of Related Structures:  
  1Z30


• PubMed Abstract: 
  

The 5'-terminal cloverleaf (CL)-like RNA structures are essential for the initiation of positive- and negative-strand RNA synthesis of entero- and rhinoviruses. SLD is the cognate RNA ligand of the viral proteinase 3C (3C(pro)), which is an indispensable component of the viral replication initiation complex. The structure of an 18mer RNA representing the apical stem and the cGUUAg D-loop of SLD from the first 5'-CL of BEV1 was determined in solution to a root-mean-square deviation (r.m.s.d.) (all heavy atoms) of 0.59 A (PDB 1Z30). The first (antiG) and last (synA) nucleotide of the D-loop forms a novel 'pseudo base pair' without direct hydrogen bonds. The backbone conformation and the base-stacking pattern of the cGUUAg-loop, however, are highly similar to that of the coxsackieviral uCACGg D-loop (PDB 1RFR) and of the stable cUUCGg tetraloop (PDB 1F7Y) but surprisingly dissimilar to the structure of a cGUAAg stable tetraloop (PDB 1MSY), even though the cGUUAg BEV D-loop and the cGUAAg tetraloop differ by 1 nt only. Together with the presented binding data, these findings provide independent experimental evidence for our model [O. Ohlenschlager, J. Wohnert, E. Bucci, S. Seitz, S. Hafner, R. Ramachandran, R. Zell and M. Gorlach (2004) Structure, 12, 237-248] that the proteinase 3C(pro) recognizes structure rather than sequence.

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Organizational Affiliation: 

Molekulare Biophysik/NMR-Spektroskopie, Institut für Molekulare Biotechnologie e.V. Beutenbergstrasse 11, D-07745 Jena, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-R(*GP*GP*CP*GP*UP*UP*CP*GP*UP*UP*AP*GP*AP*AP*CP*GP*UP*C)-3'	A	18	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 15 
• Selection Criteria: structures with the lowest energy, target function 
• OLDERADO: 1Z30 Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-03-10 
• Released Date: 2005-04-26 
Deposition Author(s): Ihle, Y., Ohlenschlager, O., Duchardt, E., Ramachandran, R., Gorlach, M.

Revision History  

• Version 1.0: 2005-04-26
  Type: Initial release
  
• Version 1.1: 2008-04-30
  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