5XWG

Crystal structure of a novel RNA motif that allows for precise positioning of a metal ion

  • Classification: RNA
  • Organism(s): synthetic construct

  • Deposited: 2017-06-29 Released: 2017-10-11 
  • Deposition Author(s): Kanazawa, H., Kondo, J.
  • Funding Organization(s): the Ichiro Kanehara Foundation; AMED; the Japan Science Society 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.002 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structure of a novel RNA motif that allows for precise positioning of a single metal ion.

Kanazawa, H.Kondo, J.

(2017) J. Inorg. Biochem. 176: 140-143

  • DOI: 10.1016/j.jinorgbio.2017.08.029

  • PubMed Abstract: 
  • We have determined a crystal structure of an RNA duplex containing a novel metal-binding motif. The motif is composed of two sheared G○A base pairs, two unpaired A residues and four phosphate groups in close proximity. Four A residues make an A-A-A-A ...

    We have determined a crystal structure of an RNA duplex containing a novel metal-binding motif. The motif is composed of two sheared G○A base pairs, two unpaired A residues and four phosphate groups in close proximity. Four A residues make an A-A-A-A stacking column at the minor groove side and two G bases are highly inclined, thereby forming the pocket-shaped motif at the major groove side. In the present structure, a hydrated Sr2+ ion exists in the pocket and binds to the O6 and N7 atoms of the two G bases and four phosphate groups. According to the previously-reported metal-binding properties to RNA molecules, many of divalent cations, such as Mg2+, Mn2+, Co2+, Zn2+, Ba2+, Pb2+ and Cd2+, may bind to the motif. This metal-binding motif can be used as a modular building block that allows for precise positioning of a single metal ion in functional nucleic acid molecules.


    Organizational Affiliation

    Graduate School of Science and Technology, Sophia University, Tokyo 102-8554, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA (5'-R(P*CP*GP*CP*UP*(5BU)P*CP*GP*AP*AP*AP*AP*AP*GP*UP*C)-3')A15synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SR
Query on SR

Download SDF File 
Download CCD File 
A
STRONTIUM ION
Sr
PWYYWQHXAPXYMF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
5BU
Query on 5BU
A
RNA LINKINGC9 H12 Br N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.002 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.217 
  • Space Group: I 21 3
Unit Cell:
Length (Å)Angle (°)
a = 80.544α = 90.00
b = 80.544β = 90.00
c = 80.544γ = 90.00
Software Package:
Software NamePurpose
AutoSolphasing
SCALAdata scaling
CrystalCleardata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
the Ichiro Kanehara FoundationJapan--
AMEDJapan--
the Japan Science SocietyJapan--

Revision History 

  • Version 1.0: 2017-10-11
    Type: Initial release