3ZP8

HIGH-RESOLUTION FULL-LENGTH HAMMERHEAD RIBOZYME


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Active-Site Monovalent Cations Revealed in a 1.55 A Resolution Hammerhead Ribozyme Structure

Anderson, M.Schultz, E.Martick, M.Scott, W.G.

(2013) J.Mol.Biol. 425: 3790

  • DOI: 10.1016/j.jmb.2013.05.017

  • PubMed Abstract: 
  • We have obtained a 1.55-Å crystal structure of a hammerhead ribozyme derived from Schistosoma mansoni under conditions that permit detailed observations of Na(+) ion binding in the ribozyme's active site. At least two such Na(+) ions are observed. Th ...

    We have obtained a 1.55-Å crystal structure of a hammerhead ribozyme derived from Schistosoma mansoni under conditions that permit detailed observations of Na(+) ion binding in the ribozyme's active site. At least two such Na(+) ions are observed. The first Na(+) ion binds to the N7 of G10.1 and the adjacent A9 phosphate in a manner identical with that previously observed for divalent cations. A second Na(+) ion binds to the Hoogsteen face of G12, the general base in the hammerhead cleavage reaction, thereby potentially dissipating the negative charge of the catalytically active enolate form of the nucleotide base. A potential but more ambiguous third site bridges the A9 and scissile phosphates in a manner consistent with that of previous predictions. Hammerhead ribozymes have been observed to be active in the presence of high concentrations of monovalent cations, including Na(+), but the mechanism by which monovalent cations substitute for divalent cations in hammerhead catalysis remains unclear. Our results enable us to suggest that Na(+) directly and specifically substitutes for divalent cations in the hammerhead active site. The detailed geometry of the pre-catalytic active-site complex is also revealed with a new level of precision, thanks to the quality of the electron density maps obtained from what is currently the highest-resolution ribozyme structure in the Protein Data Bank.


    Organizational Affiliation

    Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA, 228 Sinsheimer Laboratories, University of California at Santa Cruz, Santa Cruz, CA 95064, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
HAMMERHEAD RIBOZYME, ENZYME STRANDA43synthetic construct
Entity ID: 2
MoleculeChainsLengthOrganism
HAMMERHEAD RIBOZYME, SUBSTRATE STRANDB20synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
GDP
Query on GDP
A
RNA LINKINGC10 H15 N5 O11 P2G
OMC
Query on OMC
B
RNA LINKINGC10 H16 N3 O8 PC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.187 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 50.820α = 90.00
b = 68.530β = 112.35
c = 58.900γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-03-06
    Type: Initial release
  • Version 1.1: 2013-06-05
    Type: Database references
  • Version 1.2: 2013-10-30
    Type: Database references