3CZW

X-ray structures of the (GUGGUCUGAUGAGGCC) RNA duplex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Noncanonical G(syn)-G(anti) base pairs stabilized by sulphate anions in two X-ray structures of the (GUGGUCUGAUGAGGCC) RNA duplex.

Rypniewski, W.Adamiak, D.A.Milecki, J.Adamiak, R.W.

(2008) Rna 14: 1845-1851

  • DOI: 10.1261/rna.1164308
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The structures of two crystal forms of the RNA 16-mer with the sequence GUGGUCUGAUGAGGCC, grown in the presence of a high concentration of sulphate ions, have been determined using synchrotron radiation at 1.4- and 2.0-A resolution. RNA with this seq ...

    The structures of two crystal forms of the RNA 16-mer with the sequence GUGGUCUGAUGAGGCC, grown in the presence of a high concentration of sulphate ions, have been determined using synchrotron radiation at 1.4- and 2.0-A resolution. RNA with this sequence is known as one of the two strands of the noncleavable form of the hammerhead ribozyme. In both crystal structures, two G(syn)-G(anti) noncanonical base pairs are observed in the middle of a 14 base-pair (bp) duplex having 5'-dangling GU residues. Both structures contain sulphate anions interacting with the G-G bp stabilizing G in its syn conformation and bridging the two RNA strands. In both cases the interactions take place in the major groove, although the anions are accommodated within different helix geometries, most pronounced in the changing width of the major groove. In one structure, where a single sulphate spans both G-G pairs, the major groove is closed around the anion, while in the other structure, where each of the two G-G pairs is associated with a separate sulphate, the groove is open. This work provides the first examples of a G-G pair in syn-anti conformation, which minimizes the purine-purine clash in the center of the duplex, while utilizing its residual hydrogen bonding potential in specific interactions with sulphate anions.


    Organizational Affiliation

    Institute of Bioorganic Chemistry, Polish Academy of Sciences, PoznaƄ , Poland.




Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganism
RNA (5'-R(*G*UP*GP*GP*UP*CP*UP*GP*AP*UP*GP*AP*GP*GP*CP*C)-3')X16N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
X
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.197 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 56.035α = 90.00
b = 31.863β = 134.35
c = 39.804γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
MOLREPphasing
MAR345data collection
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-09-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description