4PCO

Crystal structure of double-stranded RNA with four terminal GU wobble base pairs

  • Classification: RNA
  • Organism(s): Endothia gyrosa

  • Deposited: 2014-04-15 Released: 2015-10-14 
  • Deposition Author(s): Mooers, B.H.M.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures and Energetics of Four Adjacent GU Pairs That Stabilize an RNA Helix.

Gu, X.Mooers, B.H.Thomas, L.M.Malone, J.Harris, S.Schroeder, S.J.

(2015) J.Phys.Chem.B 119: 13252-13261

  • DOI: 10.1021/acs.jpcb.5b06970

  • PubMed Abstract: 
  • Consecutive G·U base pairs inside RNA helices can be destabilizing, while those at the ends of helices are thermodynamically stabilizing. To determine if this paradox could be explained by differences in base stacking, we determined the high-resoluti ...

    Consecutive G·U base pairs inside RNA helices can be destabilizing, while those at the ends of helices are thermodynamically stabilizing. To determine if this paradox could be explained by differences in base stacking, we determined the high-resolution (1.32 Å) crystal structure of (5'-GGUGGCUGUU-3')2 and studied three sequences with four consecutive terminal G·U pairs by NMR spectroscopy. In the crystal structure of (5'-GGUGGCUGUU-3')2, the helix is overwound but retains the overall features of A-form RNA. The penultimate base steps at each end of the helix have high base overlap and contribute to the unexpectedly favorable energetic contribution for the 5'-GU-3'/3'-UG-5' motif in this helix position. The balance of base stacking and helical twist contributes to the positional dependence of G·U pair stabilities. The energetic stabilities and similarity to A-form RNA helices suggest that consecutive G·U pairs would be recognized by RNA helix binding proteins, such as Dicer and Ago. Thus, these results will aid future searches for target sites of small RNAs in gene regulation.


    Organizational Affiliation

    Department of Chemistry and Biochemistry and ‡Department of Microbiology and Plant Biology, University of Oklahoma , Norman, Oklahoma 73019, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA (5'-D(*GP*GP*UP*GP*GP*CP*UP*GP*UP*U)-3')A,B,C,D,E10Endothia gyrosa
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NCO
Query on NCO

Download SDF File 
Download CCD File 
A, B, C, D, E
COBALT HEXAMMINE(III)
Co H18 N6
DYLMFCCYOUSRTK-FGTKAUEHAT
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.155 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 36.616α = 90.00
b = 43.224β = 102.48
c = 83.256γ = 90.00
Software Package:
Software NamePurpose
SHELXphasing
SCALAdata scaling
SHELXDphasing
SHELXphasing
PDB_EXTRACTdata extraction
Cootmodel building
Blu-Icedata collection
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2014-04-15 
  • Released Date: 2015-10-14 
  • Deposition Author(s): Mooers, B.H.M.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesR01-AI088011

Revision History 

  • Version 1.0: 2015-10-14
    Type: Initial release
  • Version 1.1: 2016-01-27
    Type: Database references
  • Version 1.2: 2017-09-06
    Type: Author supporting evidence, Database references, Derived calculations