6E7L

Structure of a dimerized UUCG motif

• PDB DOI: https://doi.org/10.2210/pdb6E7L/pdb
• NAKB: 6E7L

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


• Deposited: 2018-07-26 Released: 2019-07-31 
• Deposition Author(s): Montemayor, E.J., Butcher, S.E.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 0.210 
• R-Value Work: 0.176 
• R-Value Observed: 0.179 

Literature

Structure of an RNA helix with pyrimidine mismatches and cross-strand stacking.

Montemayor, E.J., Virta, J.M., Hagler, L.D., Zimmerman, S.C., Butcher, S.E.

(2019) Acta Crystallogr F Struct Biol Commun 75: 652-656

• PubMed: 31584014 
• DOI: https://doi.org/10.1107/S2053230X19012172
• Primary Citation of Related Structures:  
  6E7L


• PubMed Abstract: 
  

  The structure of a 22-base-pair RNA helix with mismatched pyrimidine base pairs is reported. The helix contains two symmetry-related CUG sequences: a triplet-repeat motif implicated in myotonic dystrophy type 1. The CUG repeat contains a U-U mismatch sandwiched between Watson-Crick pairs. Additionally, the center of the helix contains a dimerized UUCG motif with tandem pyrimidine (U-C/C-U) mismatches flanked by U-G wobble pairs. This region of the structure is significantly different from previously observed structures that share the same sequence and neighboring base pairs. The tandem pyrimidine mismatches are unusual and display sheared, cross-strand stacking geometries that locally constrict the helical width, a type of stacking previously associated with purines in internal loops. Thus, pyrimidine-rich regions of RNA have a high degree of structural diversity.

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Organizational Affiliation: 

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

Biological Assembly 1  

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

Macromolecule Content

• Total Structure Weight: 7.02 kDa 
• Atom Count: 474 
• Modelled Residue Count: 22 
• Deposited Residue Count: 22 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*GP*GP*GP*CP*UP*GP*CP*AP*CP*UP*UP*CP*GP*GP*UP*GP*CP*UP*GP*CP*CP*C)-3')	A	22	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 0.210 
• R-Value Work: 0.176 
• R-Value Observed: 0.179 
• Space Group: P 4₁ 2₁ 2
• Diffraction Data: https://doi.org/10.15785/SBGRID/712

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.041	α = 90
b = 42.041	β = 90
c = 77.86	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-07-31 
Deposition Author(s): Montemayor, E.J., Butcher, S.E.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM118131
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)	United States	R01 AR069645
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P41 GM103403

Revision History  

• Version 1.0: 2019-07-31
  Type: Initial release
  
• Version 1.1: 2019-10-16
  Changes: Data collection, Database references
• Version 1.2: 2019-11-13
  Changes: Database references
• Version 1.3: 2019-12-11
  Changes: Author supporting evidence
• Version 1.4: 2024-03-13
  Changes: Data collection, Database references
• Version 1.5: 2024-04-03
  Changes: Refinement description