2LBS

Solution structure of double-stranded RNA binding domain of S. cerevisiae RNase III (Rnt1p) in complex with AAGU tetraloop hairpin

• PDB DOI:  https://doi.org/10.2210/pdb2LBS/pdb
• NAKB: 2LBS
• BMRB: 17574

• Classification: HYDROLASE/RNA
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2011-04-06 Released: 2011-08-31 
• Deposition Author(s): Wang, Z., Hartman, E., Roy, K., Chanfreau, G., Feigon, J.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 16 
• Selection Criteria: structures with the lowest energy 

Literature

Structure of a Yeast RNase III dsRBD Complex with a Noncanonical RNA Substrate Provides New Insights into Binding Specificity of dsRBDs.

Wang, Z., Hartman, E., Roy, K., Chanfreau, G., Feigon, J.

(2011) Structure 19: 999-1010

• PubMed: 21742266 
• DOI: https://doi.org/10.1016/j.str.2011.03.022
• Primary Citation of Related Structures:  
  2LBS, 2LUP


• PubMed Abstract: 
  

dsRBDs often bind dsRNAs with some specificity, yet the basis for this is poorly understood. Rnt1p, the major RNase III in Saccharomyces cerevisiae, cleaves RNA substrates containing hairpins capped by A/uGNN tetraloops, using its dsRBD to recognize a conserved tetraloop fold. However, the identification of a Rnt1p substrate with an AAGU tetraloop raised the question of whether Rnt1p binds to this noncanonical substrate differently than to A/uGNN tetraloops. The solution structure of Rnt1p dsRBD bound to an AAGU-capped hairpin reveals that the tetraloop undergoes a structural rearrangement upon binding to Rnt1p dsRBD to adopt a backbone conformation that is essentially the same as the AGAA tetraloop, and indicates that a conserved recognition mode is used for all Rnt1p substrates. Comparison of free and RNA-bound Rnt1p dsRBD reveals that tetraloop-specific binding requires a conformational change in helix α1. Our findings provide a unified model of binding site selection by this dsRBD.

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Related Citations: 

• Structural basis for recognition of the AGNN tetraloop RNA fold by the double-stranded RNA-binding domain of Rnt1p RNase III
  Wu, H., Henras, A., Chanfreau, G., Feigon, J.
  (2004) Proc Natl Acad Sci U S A 101: 8307

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, P.O. Box 951569, University of California, Los Angeles, CA 90095-1569, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 20.1 kDa 
• Atom Count: 1,368 
• Modelled Residue Count: 122 
• Deposited Residue Count: 122 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease 3	B	90	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: RNT1, YM9408.01C, YM9959.21, YMR239C EC: 3.1.26.3
UniProt
Find proteins for Q02555 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q02555  Go to UniProtKB:  Q02555

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (32-MER)	A	32	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 16 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-31 
Deposition Author(s): Wang, Z., Hartman, E., Roy, K., Chanfreau, G., Feigon, J.

Revision History  

• Version 1.0: 2011-08-31
  Type: Initial release