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1m5k, resolution 2.40Å ()
Ligands: ,
Non-Standard Residues: , ,
Gene: SNRPA (Homo sapiens)
Related: 1m5o, 1m5p, 1m5v
Resources: FirstGlance, OCA, PDBsum, RCSB
Coordinates: save as pdb, mmCIF, xml


Crystal structure of a hairpin ribozyme in the catalytically-active conformation

Publication Abstract from PubMed

The hairpin ribozyme catalyses sequence-specific cleavage of RNA. The active site of this natural RNA results from the docking of two irregular helices: stems A and B. One strand of stem A harbours the scissile bond. The 2.4 A resolution structure of a hairpin ribozyme-inhibitor complex reveals that the ribozyme aligns the 2'-OH nucleophile and the 5'-oxo leaving group by twisting apart the nucleotides that flank the scissile phosphate. The base of the nucleotide preceding the cleavage site is stacked within stem A; the next nucleotide, a conserved guanine, is extruded from stem A and accommodated by a highly complementary pocket in the minor groove of stem B. Metal ions are absent from the active site. The bases of four conserved purines are positioned potentially to serve as acid-base catalysts. This is the first structure determination of a fully assembled ribozyme active site that catalyses a phosphodiester cleavage without recourse to metal ions.

Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis., Rupert PB, Ferre-D'Amare AR, Nature. 2001 Apr 12;410(6830):780-6. PMID:11298439

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

About this Structure

1m5k is a 6 chain structure with sequence from Homo sapiens. This structure supersedes the now removed PDB entry 1hp6. Full crystallographic information is available from OCA.

See Also


  • Rupert PB, Ferre-D'Amare AR. Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis. Nature. 2001 Apr 12;410(6830):780-6. PMID:11298439 doi:10.1038/35071009
  • Rupert PB, Massey AP, Sigurdsson ST, Ferre-D'Amare AR. Transition state stabilization by a catalytic RNA. Science. 2002 Nov 15;298(5597):1421-4. Epub 2002 Oct 10. PMID:12376595 doi:

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