Macromolecule Content

• Total Structure Weight: 20.13 kDa 
• Atom Count: 1370 
• Residue Count: 122 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

1T4L

Solution structure of double-stranded RNA binding domain of S. cerevisiae RNase III (Rnt1p) in complex with the 5' terminal RNA hairpin of snR47 precursor

• DOI: 10.2210/pdb1T4L/pdb
• NDB: 1T4L

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


• Deposited: 2004-04-29 Released: 2004-06-01 
• Deposition Author(s): Wu, H., Henras, A., Chanfreau, G., Feigon, J.

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Experimental Data Snapshot

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

Literature

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: 8307-8312

• PubMed: 15150409 
• DOI: 10.1073/pnas.0402627101
• Primary Citation of Related Structures:  
  1T4L


• PubMed Abstract: 
  

Specific recognition of double-stranded RNA (dsRNA) by dsRNA-binding domains (dsRBDs) is involved in a large number of biological and regulatory processes. Although structures of dsRBDs in complex with dsRNA have revealed how they can bind to dsRNA in general, these do not explain how a dsRBD can recognize specific RNAs. Rnt1p, a member of the RNase III family of dsRNA endonucleases, is a key component of the Saccharomyces cerevisiae RNA-processing machinery. The Rnt1p dsRBD has been implicated in targeting this endonuclease to its RNA substrates, by recognizing hairpins closed by AGNN tetraloops. We report the solution structure of Rnt1p dsRBD complexed to the 5' terminal hairpin of one of its small nucleolar RNA substrates, the snR47 precursor. The conserved AGNN tetraloop fold is retained in the protein-RNA complex. The dsRBD contacts the RNA at successive minor, major, and tetraloop minor grooves on one face of the helix. Surprisingly, neither the universally conserved G nor the highly conserved A are recognized by specific hydrogen bonds to the bases. Rather, the N-terminal helix fits snugly into the minor groove of the RNA tetraloop and top of the stem, interacting in a non-sequence-specific manner with the sugar-phosphate backbone and the two nonconserved tetraloop bases. Mutational analysis of residues that contact the tetraloop region show that they are functionally important for RNA processing in the context of the entire protein in vivo. These results show how a single dsRBD can convey specificity for particular RNA targets, by structure specific recognition of a conserved tetraloop fold.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry and Molecular Biology Institute, University of California, Los Angeles, CA 90095-1569, USA.

Macromolecules

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

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5' terminal hairpin of snR47 precursor	A	32	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 15 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 1T4L Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-04-29 
• Released Date: 2004-06-01 
Deposition Author(s): Wu, H., Henras, A., Chanfreau, G., Feigon, J.

Revision History 

• Version 1.0: 2004-06-01
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance