1A9L

SOLUTION STRUCTURE OF A SUBSTRATE FOR THE ARCHAEAL PRE-TRNA SPLICING ENDONUCLEASES: THE BULGE-HELIX-BULGE MOTIF, NMR, 12 STRUCTURES

• PDB DOI: https://doi.org/10.2210/pdb1A9L/pdb
• NAKB: 1A9L

• Classification: RNA
• Mutation(s): No 


• Deposited: 1998-04-07 Released: 1998-06-17 
• Deposition Author(s): Diener, J.L., Moore, P.B.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 65 
• Conformers Submitted: 12 
• Selection Criteria: LEAST RESTRAINT VIOLATION 

Literature

Solution structure of a substrate for the archaeal pre-tRNA splicing endonucleases: the bulge-helix-bulge motif.

Diener, J.L., Moore, P.B.

(1998) Mol Cell 1: 883-894

• PubMed: 9660971 
• Primary Citation of Related Structures:  
  1A9L, 2A9L


• PubMed Abstract: 
  

  The structure of the bulge-helix-bulge motif that constitutes the intron/exon splice site in H. volcanii pre-tRNATrp has been determined by NMR spectroscopy. The conformations of the two 3 nt bulges, where the pre-tRNA is cleaved, are stabilized by stacking interactions between bulge nucleotides and bases in the adjacent Watson-Crick helices and by a network of backbone hydrogen bonds. Both bulges are presented on the same minor groove face of the central 4 bp helix, and the overall structure has approximate two-fold symmetry, which makes it well-suited for attack by archaeal splicing endonucleases, which are symmetric dimers.

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Organizational Affiliation: 

Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 12.32 kDa 
• Atom Count: 816 
• Modelled Residue Count: 38 
• Deposited Residue Count: 38 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
PRE-TRNA BULGE-HELIX-BULGE MOTIF	A	38	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 65 
• Conformers Submitted: 12 
• Selection Criteria: LEAST RESTRAINT VIOLATION 

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-06-17 
Deposition Author(s): Diener, J.L., Moore, P.B.

Revision History  

• Version 1.0: 1998-06-17
  Type: Initial release
  
• Version 1.1: 2008-03-05
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-02-16
  Changes: Database references, Derived calculations, Other
• Version 1.4: 2024-05-22
  Changes: Data collection