Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 12.41 kDa 
• Atom Count: 876 
• Modelled Residue Count: 38 
• Deposited Residue Count: 38 
• Unique nucleic acid chains: 1

4YN6

Structural Insight reveals dynamics in repeating r(CAG) transcript found in Huntington's disease (HD) and Spinocerebellar ataxias (SCAs)

• PDB DOI: 10.2210/pdb4YN6/pdb
• NDB: 4YN6

• Classification: RNA
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2015-03-09 Released: 2015-04-22 
• Deposition Author(s): Tawani, A., Kumar, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.261 
• R-Value Work: 0.217 
• R-Value Observed: 0.219 

Literature

Structural Insights Reveal the Dynamics of the Repeating r(CAG) Transcript Found in Huntington's Disease (HD) and Spinocerebellar Ataxias (SCAs)

Tawani, A., Kumar, A.

(2015) PLoS One 10: e0131788-e0131788

• PubMed: 26148061 
• DOI: 10.1371/journal.pone.0131788
• Primary Citation of Related Structures:  
  2MS5, 4YN6


• PubMed Abstract: 
  

In humans, neurodegenerative disorders such as Huntington's disease (HD) and many spinocerebellar ataxias (SCAs) have been found to be associated with CAG trinucleotide repeat expansion. An important RNA-mediated mechanism that causes these diseases involves the binding of the splicing regulator protein MBNL1 (Muscleblind-like 1 protein) to expanded r(CAG) repeats. Moreover, mutant huntingtin protein translated from expanded r(CAG) also yields toxic effects. To discern the role of mutant RNA in these diseases, it is essential to gather information about its structure. Detailed insight into the different structures and conformations adopted by these mutant transcripts is vital for developing therapeutics targeting them. Here, we report the crystal structure of an RNA model with a r(CAG) motif, which is complemented by an NMR-based solution structure obtained from restrained Molecular Dynamics (rMD) simulation studies. Crystal structure data of the RNA model resolved at 2.3 Å reveals non-canonical pairing of adenine in 5´-CAG/3´-GAC motif samples in different syn and anti conformations. The overall RNA structure has helical parameters intermediate to the A- and B-forms of nucleic acids due to the global widening of major grooves and base-pair preferences near internal AA loops. The comprehension of structural behaviour by studying the spectral features and the dynamics also supports the flexible nature of the r(CAG) motif.

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Organizational Affiliation: 

Centre for Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India.

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*UP*UP*GP*GP*GP*CP*CP*AP*GP*CP*AP*GP*CP*AP*GP*GP*UP*CP*C)-3')	A, B	19	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A], D [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.261 
• R-Value Work: 0.217 
• R-Value Observed: 0.219 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.074	α = 90
b = 46.074	β = 90
c = 133.202	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
Coot	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-03-09 
• Released Date: 2015-04-22 
Deposition Author(s): Tawani, A., Kumar, A.

Revision History  

• Version 1.0: 2015-04-22
  Type: Initial release
  
• Version 1.1: 2015-04-29
  Changes: Data collection
• Version 1.2: 2015-07-15
  Changes: Database references
• Version 1.3: 2015-09-02
  Changes: Data collection