3D0M

X-ray structures of the (GUGGUCUGAUGAGGCC) RNA duplex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.361 
  • R-Value Work: 0.295 

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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:  
    3CZW, 3D0M

  • 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 sequence is known as one of the two strands of the noncleavable form of the hammerhead ribozyme ...

    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, Poznań , Poland.



Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganismImage
RNA (5'-R(*GP*UP*GP*GP*UP*CP*UP*GP*AP*UP*GP*AP*GP*GP*CP*C)-3')A [auth X]16N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download Ideal Coordinates CCD File 
B [auth X]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.361 
  • R-Value Work: 0.295 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.653α = 90
b = 46.653β = 90
c = 126.397γ = 120
Software Package:
Software NamePurpose
MAR345data collection
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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