Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 38.73 kDa 
• Atom Count: 2,375 
• Modelled Residue Count: 168 
• Deposited Residue Count: 175 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

 2OIH

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

• PDB DOI: 10.2210/pdb2OIH/pdb
• NDB: PR0260

• Classification: structural protein/RNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-01-11 Released: 2007-03-27 
• Deposition Author(s): Ke, A., Ding, F., Batchelor, J.D., Doudna, J.A.

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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 

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

• PubMed: 17355864 
• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
U1 small nuclear ribonucleoprotein A	B [auth A]	100	Homo sapiens	Mutation(s): 0  Gene Names: SNRPA
UniProt & NIH Common Fund Data Resources
Find proteins for P09012 (Homo sapiens) Explore P09012  Go to UniProtKB:  P09012
PHAROS:  P09012

Entity ID: 1
Molecule	Chains	Length	Organism	Image
HDV ribozyme	A [auth B]	75	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TL	C [auth B], D [auth B], E [auth B], F [auth B], G [auth B], H [auth B], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B]	THALLIUM (I) ION Tl ZLUSCZLCHQSJRU-UHFFFAOYSA-N

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 = 107.962	α = 90
b = 107.962	β = 90
c = 189.119	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-03-27 
Deposition Author(s): Ke, A., Ding, F., Batchelor, J.D., Doudna, J.A.

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