4PCO

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

  • Classification: RNA
  • Organism(s): Endothia gyrosa
  • Mutation(s): No 

  • 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 (NIH/NIAID)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 

wwPDB Validation   3D Report Full Report


This is version 1.4 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: https://doi.org/10.1021/acs.jpcb.5b06970
  • Primary Citation of Related Structures:  
    4PCO

  • 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-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 nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (5'-D(*GP*GP*UP*GP*GP*CP*UP*GP*UP*U)-3')
A, B, C, D, E
10Endothia gyrosa
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NCO
Query on NCO

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
K [auth B]
L [auth B]
F [auth A],
G [auth A],
H [auth A],
K [auth B],
L [auth B],
M [auth B],
O [auth C],
P [auth C],
Q [auth C],
R [auth D],
S [auth E],
T [auth E]
COBALT HEXAMMINE(III)
Co H18 N6
DYLMFCCYOUSRTK-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
N [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.616α = 90
b = 43.224β = 102.48
c = 83.256γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SHELXphasing
SHELXphasing
PDB_EXTRACTdata extraction
Cootmodel building
Blu-Icedata collection
SCALAdata scaling
SHELXDphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01-AI088011

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-14
    Type: Initial release
  • Version 1.1: 2016-01-27
    Changes: Database references
  • Version 1.2: 2017-09-06
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.3: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.4: 2023-12-27
    Changes: Data collection, Database references