6CHR

Crystal structure of a group II intron lariat with an intact 3' splice site (pre-2s state)

Summary for 6CHR

• Entry DOI: 10.2210/pdb6chr/pdb
• Descriptor: RNA (621-MER), RNA (5'-R(P*UP*GP*UP*UP*UP*AP*UP*UP*AP*AP*AP*AP*A)-3'), MAGNESIUM ION, ... (6 entities in total)
• Functional Keywords: group ii intron, rna splicing, spliceosome, lariat 3'-exon, rna
• Biological source: Pylaiella littoralis; More
• Total number of polymer chains: 2
• Total formula weight: 208636.49

Authors

Chan, R.T.,Peters, J.K.,Robart, A.R.,Wiryaman, T.,Rajashankar, K.R.,Toor, N. (deposition date: 2018-02-22, release date: 2018-11-21, Last modification date: 2024-03-13)

Primary citation

Chan, R.T.,Peters, J.K.,Robart, A.R.,Wiryaman, T.,Rajashankar, K.R.,Toor, N.
Structural basis for the second step of group II intron splicing.
Nat Commun, 9:4676-4676, 2018

PubMed Abstract: The group II intron and the spliceosome share a common active site architecture and are thought to be evolutionarily related. Here we report the 3.7 Å crystal structure of a eukaryotic group II intron in the lariat-3' exon form, immediately preceding the second step of splicing, analogous to the spliceosomal P complex. This structure reveals the location of the intact 3' splice site within the catalytic core of the group II intron. The 3'-OH of the 5' exon is positioned in close proximity to the 3' splice site for nucleophilic attack and exon ligation. The active site undergoes conformational rearrangements with the catalytic triplex having different configurations before and after the second step of splicing. We describe a complete model for the second step of group II intron splicing that incorporates a dynamic catalytic triplex being responsible for creating the binding pocket for 3' splice site capture.

PubMed: 30410046
DOI: 10.1038/s41467-018-06678-0

Experimental method

X-RAY DIFFRACTION (3.7 Å)