Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 7.71 kDa 
• Atom Count: 510 
• Modelled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

1NC0

U80G U6 Intramolecular Stem-Loop RNA from Saccharomyces cerevisiae

• PDB DOI: 10.2210/pdb1NC0/pdb
• NDB: 1NC0
• BMRB: 5655

• Classification: RNA
• Mutation(s): No 


• Deposited: 2002-12-04 Released: 2003-02-25 
• Deposition Author(s): Sashital, D.G., Allmann, A.M., Van Doren, S., Butcher, S.E.

---

Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Submitted: 18 

Literature

Structural Basis for a Lethal Mutation in U6 RNA

Sashital, D.G., Allmann, A.M., Van Doren, S., Butcher, S.E.

(2003) Biochemistry 42: 1470-1477

• PubMed: 12578359 
• DOI: 10.1021/bi027137h
• Primary Citation of Related Structures:  
  1NC0


• PubMed Abstract: 
  

U6 RNA is essential for nuclear pre-mRNA splicing and has been implicated directly in catalysis of intron removal. The U80G mutation at the essential magnesium binding site of the U6 3' intramolecular stem-loop region (ISL) is lethal in yeast. To further understand the structure and function of the U6 ISL, we have investigated the structural basis for the lethal U80G mutation by NMR and optical spectroscopy. The NMR structure reveals that the U80G mutation causes a structural rearrangement within the ISL resulting in the formation of a new Watson-Crick base pair (C67 x G80), and disrupts a protonated C67 x A79 wobble pair that forms in the wild-type structure. Despite the structural change, the accessibility of the metal binding site is unperturbed, and cadmium titration produces similar phosphorus chemical shift changes for both the U80G mutant and wild-type RNAs. The thermodynamic stability of the U80G mutant is significantly increased (Delta Delta G(fold) = -3.6 +/- 1.9 kcal/mol), consistent with formation of the Watson-Crick pair. Our structural and thermodynamic data, in combination with previous genetic data, suggest that the lethal basis for the U80G mutation is stem-loop hyperstabilization. This hyperstabilization may prevent the U6 ISL melting and rearrangement necessary for association with U4.

---

Organizational Affiliation: 

Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
U80G U6 RNA Intramolecular Stem-Loop	A	24	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Submitted: 18 
• OLDERADO: 1NC0 Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-12-04 
• Released Date: 2003-02-25 
Deposition Author(s): Sashital, D.G., Allmann, A.M., Van Doren, S., Butcher, S.E.

Revision History  

• Version 1.0: 2003-02-25
  Type: Initial release
  
• Version 1.1: 2008-04-28
  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