1I3Y | pdb_00001i3y

SOLUTION STRUCTURE OF THE A LOOP OF 23S RIBOSOMAL RNA.

• PDB DOI: https://doi.org/10.2210/pdb1I3Y/pdb
• NAKB: 1I3Y

• Classification: RNA
• Mutation(s): No 


• Deposited: 2001-02-17 Released: 2001-04-04 
• Deposition Author(s): Puglisi, J.D., Blanchard, S.C.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 46 
• Conformers Submitted: 21 
• Selection Criteria: structures with the lowest energy 

Literature

Solution structure of the A loop of 23S ribosomal RNA.

Blanchard, S.C., Puglisi, J.D.

(2001) Proc Natl Acad Sci U S A 98: 3720-3725

• PubMed: 11259644 
• DOI: https://doi.org/10.1073/pnas.051608498
• Primary Citation Related Structures: 
  1I3X, 1I3Y


• PubMed Abstract: 
  

  The A loop is an essential RNA component of the ribosome peptidyltransferase center that directly interacts with aminoacyl (A)-site tRNA. The A loop is highly conserved and contains a ubiquitous 2'-O-methyl ribose modification at position U2552. Here, we present the solution structure of a modified and unmodified A-loop RNA to define both the A-loop fold and the structural impact of the U2552 modification. Solution data reveal that the A-loop RNA has a compact structure that includes a noncanonical base pair between C2556 and U2552. NMR evidence is presented that the N3 position of C2556 has a shifted pKa and that protonation at C2556-N3 changes the C-U pair geometry. Our data indicate that U2552 methylation modifies the A-loop fold, in particular the dynamics and position of residues C2556 and U2555. We compare our structural data with the structure of the A loop observed in a recent 50S crystal structure [Ban, N., Nissen, P., Hansen, J., Moore, P. B. & Steitz, T. A. (2000) Science 289, 905--920; Nissen, P., Hansen, J., Ban, N., Moore, P. B. & Steitz, T. A. (2000) Science 289, 920--930]. The solution and crystal structures of the A loop are dramatically different, suggesting that a structural rearrangement of the A loop must occur on docking into the peptidyltransferase center. Possible roles of this docking event, the shifted pKa of C2556 and the U2552 2'-O-methylation in the mechanism of translation, are discussed.

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Organizational Affiliation: 
• Stanford University School of Medicine, Department of Structural Biology, 299 Campus Drive West, Fairchild Building, Stanford, CA 94305-5126, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 6.08 kDa 
• Atom Count: 401 
• Modeled Residue Count: 19 
• Deposited Residue Count: 19 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-R(*GP*GP*CP*UP*GP*GP*CP*(OMU)P*GP*UP*UP*CP*GP*CP*CP*AP*GP*CP*C)-3'	A	19	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 46 
• Conformers Submitted: 21 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-04-04 
Deposition Author(s): Puglisi, J.D., Blanchard, S.C.

Revision History  

• Version 1.0: 2001-04-04
  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: Database references, Derived calculations
• Version 1.4: 2024-05-22
  Changes: Data collection