1K6H | pdb_00001k6h

Solution Structure of Conserved AGNN Tetraloops: Insights into Rnt1p RNA processing

• PDB DOI: https://doi.org/10.2210/pdb1K6H/pdb
• NAKB: 1K6H

• Classification: RNA
• Mutation(s): No 


• Deposited: 2001-10-16 Released: 2001-12-19 
• Deposition Author(s): Lebars, I., Lamontagne, B., Yoshizawa, S., Abou Elela, S., Fourmy, D.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 25 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Solution structure of conserved AGNN tetraloops: insights into Rnt1p RNA processing.

Lebars, I., Lamontagne, B., Yoshizawa, S., Aboul-Elela, S., Fourmy, D.

(2001) EMBO J 20: 7250-7258

• PubMed: 11743001 
• DOI: https://doi.org/10.1093/emboj/20.24.7250
• Primary Citation Related Structures: 
  1K6G, 1K6H


• PubMed Abstract: 
  

  Rnt1p, the yeast orthologue of RNase III, cleaves rRNAs, snRNAs and snoRNAs at a stem capped with conserved AGNN tetraloop. Here we show that 9 bp long stems ending with AGAA or AGUC tetraloops bind to Rnt1p and direct specific but sequence-independent RNA cleavage when provided with stems longer than 13 bp. The solution structures of these two tetraloops reveal a common fold for the terminal loop stabilized by non-canonical A-A or A-C pairs and extensive base stacking. The conserved nucleotides are stacked at the 5' side of the loop, exposing their Watson-Crick and Hoogsteen faces for recognition by Rnt1p. These results indicate that yeast RNase III recognizes the fold of a conserved single-stranded tetraloop to direct specific dsRNA cleavage.

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Organizational Affiliation: 
• Laboratoire de RMN, ICSN-CNRS, 1 ave de la terrasse, F-91190 Gif-sur-Yvette, France.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 7.11 kDa 
• Atom Count: 474 
• Modeled Residue Count: 22 
• Deposited Residue Count: 22 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*GP*GP*CP*GP*UP*GP*UP*UP*CP*AP*GP*AP*AP*GP*AP*AP*CP*GP*CP*GP*CP*C)-3')	A	22	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 25 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-12-19 
Deposition Author(s): Lebars, I., Lamontagne, B., Yoshizawa, S., Abou Elela, S., Fourmy, D.

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
• Version 1.4: 2024-05-22
  Changes: Data collection