2OIH

Hepatitis Delta Virus gemonic ribozyme precursor with C75U mutation and bound to monovalent cation Tl+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.266 
  • R-Value Observed: 0.266 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural roles of monovalent cations in the HDV ribozyme.

Ke, A.Ding, F.Batchelor, J.D.Doudna, J.A.

(2007) Structure 15: 281-287

  • DOI: 10.1016/j.str.2007.01.017
  • Primary Citation of Related Structures:  
    2OIH, 2OJ3

  • PubMed Abstract: 
  • The hepatitis delta virus (HDV) ribozyme catalyzes viral RNA self-cleavage through general acid-base chemistry in which an active-site cytidine and at least one metal ion are involved. Monovalent metal ions support slow catalysis and were proposed to ...

    The hepatitis delta virus (HDV) ribozyme catalyzes viral RNA self-cleavage through general acid-base chemistry in which an active-site cytidine and at least one metal ion are involved. Monovalent metal ions support slow catalysis and were proposed to substitute for structural, but not catalytic, divalent metal ions in the RNA. To investigate the role of monovalent cations in ribozyme structure and function, we determined the crystal structure of the precursor HDV ribozyme in the presence of thallium ions (Tl(+)). Two Tl(+) ions can occupy a previously observed divalent metal ion hexahydrate-binding site located near the scissile phosphate, but are easily competed away by cobalt hexammine, a magnesium hexahydrate mimic and potent reaction inhibitor. Intriguingly, a third Tl(+) ion forms direct inner-sphere contacts with the ribose 2'-OH nucleophile and the pro-S(p) scissile phosphate oxygen. We discuss possible structural and catalytic implications of monovalent cation binding for the HDV ribozyme mechanism.


    Organizational Affiliation

    Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
U1 small nuclear ribonucleoprotein AA100Homo sapiensMutation(s): 0 
Gene Names: SNRPA
Find proteins for P09012 (Homo sapiens)
Explore P09012 
Go to UniProtKB:  P09012
NIH Common Fund Data Resources
PHAROS  P09012
Protein Feature View
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  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
HDV ribozymeB75N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TL
Query on TL

Download CCD File 
B
THALLIUM (I) ION
Tl
ZLUSCZLCHQSJRU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.266 
  • R-Value Observed: 0.266 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.962α = 90
b = 107.962β = 90
c = 189.119γ = 120
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-03-27
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance