1JP0 | pdb_00001jp0

NMR Structure of the LP5.1 Hairpin from Bacillus RNase P RNA Refined WITHOUT Residual Dipolar Couplings

• PDB DOI: https://doi.org/10.2210/pdb1JP0/pdb
• NAKB: 1JP0

• Classification: RNA
• Mutation(s): No 


• Deposited: 2001-07-31 Released: 2002-05-01 
• Deposition Author(s): Leeper, T.C., Schmidt, F.J., Van Doren, S.R.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 28 
• Selection Criteria: structures with the lowest energy 

Literature

Structure of the UGAGAU hexaloop that braces Bacillus RNase P for action.

Leeper, T.C., Martin, M.B., Kim, H., Cox, S., Semenchenko, V., Schmidt, F.J., Van Doren, S.R.

(2002) Nat Struct Biol 9: 397-403

• PubMed: 11927952 
• DOI: https://doi.org/10.1038/nsb775
• Primary Citation Related Structures: 
  1JOX, 1JP0


• PubMed Abstract: 
  

  Long-range interactions involving the P5.1 hairpin of Bacillus RNase P RNA are thought to form a structural truss to support RNA folding and activity. We determined the structure of this element by NMR and refined the structure using residual dipolar couplings from a sample weakly oriented in a dilute liquid crystalline mixture of polyethylene glycol and hexanol. Dipolar coupling refinement improved the global precision of the structure from 1.5 to 1.2 A (to the mean), revised the bend angle between segments of the P5.1 stem and corroborated the structure of the loop region. The UGAGAU hexaloop of P5.1 contains two stacks of bases on opposite sides of the loop, distinguishing it from GNRA tetraloops. The unusual conformation of the juxtaposed uracil residues within the hexaloop may explain their requirement in transactivation assays.

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Organizational Affiliation: 
• Department of Biochemistry, 117 Schweitzer Hall, University of Missouri, Columbia, Missouri 65211, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 6.78 kDa 
• Atom Count: 448 
• Modeled Residue Count: 21 
• Deposited Residue Count: 21 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-R(*GP*GP*CP*GP*GP*UP*GP*CP*UP*GP*AP*GP*AP*UP*GP*CP*CP*CP*GP*UP*C)-3'	A	21	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 28 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-05-01 
Deposition Author(s): Leeper, T.C., Schmidt, F.J., Van Doren, S.R.

Revision History  

• Version 1.0: 2002-05-01
  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