8K8B

Solution structure of a hairpin RNA with the UUCGA loop

• PDB DOI: https://doi.org/10.2210/pdb8K8B/pdb
• NAKB: 8K8B

• Classification: RNA
• Organism(s): Mus musculus
• Mutation(s): No 


• Deposited: 2023-07-29 Released: 2024-06-05 
• Deposition Author(s): Ichijo, R., Kawai, G.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 11 
• Selection Criteria: structures with the lowest energy 

Literature

NMR analysis of a loop-bulge structure of UUCGA pentaloop.

Ichijo, R., Kawai, G.

(2024) Biochem Biophys Res Commun 691: 149327-149327

• PubMed: 38039839 
• DOI: https://doi.org/10.1016/j.bbrc.2023.149327
• Primary Citation of Related Structures:  
  8K8B, 8Y6U


• PubMed Abstract: 
  

  Although structures of many RNA loops, such as GNRA and UNCG tetraloops, were well known, it is still possible to find more RNA structures. In the present study, solution structure of an RNA fragment having UUCGA pentaloop was analyzed by NMR spectroscopy. It was found that the UUCG tetraloop is formed and the adenosine residue at the 3' side of the tetraloop is bulged out. The characteristic motif of the loop-bulge structure has also been found in other RNAs including CUUGU and CUGGC pentaloops. Along with the recently found T-hairpin structure with a UUUGAUU loop, in which UUUGA pentaloop and UU bulge are formed, the loop-bulge structures can be categorized as an RNA motif and it may be called as the integrated structure loop, I-loop.

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Organizational Affiliation: 

Graduate school of Advanced Engineering, Chiba Institute of Technology, Tsudanuma, Narashino, Chiba, 275-0016, Japan.

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: NMR Distance Restraints

Macromolecule Content

• Total Structure Weight: 6.07 kDa 
• Atom Count: 401 
• Modelled Residue Count: 19 
• Deposited Residue Count: 19 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*GP*GP*AP*UP*CP*CP*UP*UP*UP*CP*GP*AP*GP*GP*GP*AP*UP*CP*C)-3')	A	19	Mus musculus

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 11 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-05 
Deposition Author(s): Ichijo, R., Kawai, G.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-06-05
  Type: Initial release