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1sj3, resolution 2.20Å ()
Gene: SNRPA (Homo sapiens)
Related: 1cx0, 1drz, 1sj4
Resources: FirstGlance, OCA, PDBsum, RCSB
Coordinates: save as pdb, mmCIF, xml


Hepatitis Delta Virus Gemonic Ribozyme Precursor, with Mg2+ Bound

Publication Abstract from PubMed

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.

A conformational switch controls hepatitis delta virus ribozyme catalysis., Ke A, Zhou K, Ding F, Cate JH, Doudna JA, Nature. 2004 May 13;429(6988):201-5. PMID:15141216

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

About this Structure

1sj3 is a 2 chain structure with sequence from Hepatitis delta virus and Homo sapiens. Full crystallographic information is available from OCA.

See Also


  • Ke A, Zhou K, Ding F, Cate JH, Doudna JA. A conformational switch controls hepatitis delta virus ribozyme catalysis. Nature. 2004 May 13;429(6988):201-5. PMID:15141216 doi:http://dx.doi.org/10.1038/nature02522
  • Chen JH, Gong B, Bevilacqua PC, Carey PR, Golden BL. A catalytic metal ion interacts with the cleavage Site G.U wobble in the HDV ribozyme. Biochemistry. 2009 Feb 24;48(7):1498-507. PMID:19178151 doi:10.1021/bi8020108

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