8AMN

Crystal structure of AUGUGGCAU duplex with strontium ions


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure and thermodynamics of a UGG motif interacting with Ba2+ and other metal ions: accommodating changes in the RNA structure and the presence of a G(syn)-G(syn) pair.

Kiliszek, A.Pluta, M.Bejger, M.Rypniewski, W.

(2022) RNA 29: 44-54

  • DOI: https://doi.org/10.1261/rna.079414.122
  • Primary Citation of Related Structures:  
    8AMG, 8AMI, 8AMJ, 8AMK, 8AML, 8AMM, 8AMN

  • PubMed Abstract: 

    The self-complementary triplet 5'UGG3'/5'UGG3' is a particular structural motif containing noncanonical G-G pair and two U·G wobble pairs. It constitutes a specific structural and electrostatic environment attracting metal ions, particularly Ba2+ ions. Crystallographic research has shown that two Ba2+ cations are located in the major groove of the helix and interact directly with the UGG triplet. A comparison with the unliganded structure has revealed global changes in the RNA structure in the presence of metal ions, whereas thermodynamic measurements have shown increased stability. Moreover, in the structure with Ba2+, an unusual noncanonical G(syn)-G(syn) pair is observed instead of the common G(anti)-G(syn). We further elucidate the metal binding properties of the UGG/UGG triplet by performing crystallographic and thermodynamic studies using DSC and UV melting with other metal ions. The results explain the preferences of the UGG sequence for Ba2+ cations and point to possible applications of this metal-binding propensity.


  • Organizational Affiliation

    Institute of Bioorganic Chemistry.


Macromolecules

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Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')9Homo sapiens
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SR (Subject of Investigation/LOI)
Query on SR

Download Ideal Coordinates CCD File 
CA [auth B]
DA [auth C]
EA [auth C]
FA [auth E]
GA [auth G]
CA [auth B],
DA [auth C],
EA [auth C],
FA [auth E],
GA [auth G],
HA [auth H],
IA [auth I],
JA [auth L],
KA [auth M],
LA [auth M],
MA [auth O],
NA [auth Q],
OA [auth Q],
PA [auth S],
QA [auth S],
RA [auth U],
SA [auth Y],
TA [auth Y],
UA [auth a],
VA [auth b],
WA [auth d]
STRONTIUM ION
Sr
PWYYWQHXAPXYMF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 28.102α = 90
b = 90.131β = 91.394
c = 138.182γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentPoland--

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-23
    Type: Initial release
  • Version 1.1: 2023-02-01
    Changes: Database references
  • Version 1.2: 2024-02-07
    Changes: Data collection, Refinement description