Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 4.51 kDa 
• Atom Count: 299 
• Modelled Residue Count: 14 
• Deposited Residue Count: 14 
• Unique nucleic acid chains: 1

1K4A

STRUCTURE OF AGAA RNA TETRALOOP, NMR, 20 STRUCTURES

• PDB DOI: 10.2210/pdb1K4A/pdb
• NDB: 1K4A

• Classification: RNA
• Mutation(s): No 


• Deposited: 2001-10-07 Released: 2001-12-19 
• Deposition Author(s): Wu, H., Yang, P.K., Butcher, S.E., Kang, S., Chanfreau, G., Feigon, J.

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Experimental Data Snapshot

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

Literature

A novel family of RNA tetraloop structure forms the recognition site for Saccharomyces cerevisiae RNase III.

Wu, H., Yang, P.K., Butcher, S.E., Kang, S., Chanfreau, G., Feigon, J.

(2001) EMBO J 20: 7240-7249

• PubMed: 11743000 
• DOI: 10.1093/emboj/20.24.7240
• Primary Citation of Related Structures:  
  1K4A, 1K4B


• PubMed Abstract: 
  

RNases III are a family of double-stranded RNA (dsRNA) endoribonucleases involved in the processing and decay of a large number of cellular RNAs as well as in RNA interference. The dsRNA substrates of Saccharomyces cerevisiae RNase III (Rnt1p) are capped by tetraloops with the consensus sequence AGNN, which act as the primary docking site for the RNase. We have solved the solution structures of two RNA hairpins capped by AGNN tetraloops, AGAA and AGUU, using NMR spectroscopy. Both tetraloops have the same overall structure, in which the backbone turn occurs on the 3' side of the syn G residue in the loop, with the first A and G in a 5' stack and the last two residues in a 3' stack. A non-bridging phosphate oxygen and the universal G which are essential for Rnt1p binding are strongly exposed. The compared biochemical and structural analysis of various tetraloop sequences defines a novel family of RNA tetraloop fold with the consensus (U/A)GNN and implicates this conserved structure as the primary determinant for specific recognition of Rnt1p substrates.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, 405 Hilgard Avenue, PO Box 951569, University of California, Los Angeles, CA 90095-1569, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-R(*GP*GP*UP*UP*CP*AP*GP*AP*AP*GP*AP*AP*CP*C)-3'	A	14	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 1K4A Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-10-07 
• Released Date: 2001-12-19 
Deposition Author(s): Wu, H., Yang, P.K., Butcher, S.E., Kang, S., Chanfreau, G., Feigon, J.

Revision History  

• Version 1.0: 2001-12-19
  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