1SJ3

Hepatitis Delta Virus Gemonic Ribozyme Precursor, with Mg2+ Bound

• PDB DOI:  https://doi.org/10.2210/pdb1SJ3/pdb
• NAKB: 1SJ3

• Classification: TRANSLATION/RNA
• Organism(s): Hepatitis delta virus, Homo sapiens
• Expression System: Escherichia coli, Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2004-03-02 Released: 2004-05-18 
• Deposition Author(s): Ke, A., Zhou, K., Ding, F., Cate, J.H., Doudna, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.282 
• R-Value Work: 0.255 
• R-Value Observed: 0.255 

Literature

A Conformational Switch controls hepatitis delta virus ribozyme catalysis

Ke, A., Zhou, K., Ding, F., Cate, J.H., Doudna, J.A.

(2004) Nature 429: 201-205

• PubMed: 15141216 
• DOI: https://doi.org/10.1038/nature02522
• Primary Citation of Related Structures:  
  1SJ3, 1SJ4, 1SJF, 1VBX, 1VBY, 1VBZ, 1VC0, 1VC5, 1VC6


• PubMed Abstract: 
  

Ribozymes enhance chemical reaction rates using many of the same catalytic strategies as protein enzymes. In the hepatitis delta virus (HDV) ribozyme, site-specific self-cleavage of the viral RNA phosphodiester backbone requires both divalent cations and a cytidine nucleotide. General acid-base catalysis, substrate destabilization and global and local conformational changes have all been proposed to contribute to the ribozyme catalytic mechanism. Here we report ten crystal structures of the HDV ribozyme in its pre-cleaved state, showing that cytidine is positioned to activate the 2'-OH nucleophile in the precursor structure. This observation supports its proposed role as a general base in the reaction mechanism. Comparison of crystal structures of the ribozyme in the pre- and post-cleavage states reveals a significant conformational change in the RNA after cleavage and that a catalytically critical divalent metal ion from the active site is ejected. The HDV ribozyme has remarkable chemical similarity to protein ribonucleases and to zymogens for which conformational dynamics are integral to biological activity. This finding implies that RNA structural rearrangements control the reactivity of ribozymes and ribonucleoprotein enzymes.

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Organizational Affiliation: 

Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94705, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 36.01 kDa 
• Atom Count: 2,353 
• Modelled Residue Count: 168 
• Deposited Residue Count: 176 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
small nuclear ribonucleoprotein A	B [auth P]	100	Homo sapiens	Mutation(s): 2  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
precursor form of the Hepatitis Delta virus ribozyme	A [auth R]	76	Hepatitis delta virus

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth R], D [auth R]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.282 
• R-Value Work: 0.255 
• R-Value Observed: 0.255 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.731	α = 90
b = 108.731	β = 90
c = 191.726	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-05-18 
Deposition Author(s): Ke, A., Zhou, K., Ding, F., Cate, J.H., Doudna, J.A.

Revision History  

• Version 1.0: 2004-05-18
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2011-11-16
  Changes: Atomic model
• Version 1.4: 2021-10-27
  Changes: Database references, Derived calculations