Cryo-EM structure of a human spliceosome activated for step 2 of splicing

Karl Bertram; Dmitry E Agafonov; Wen-Ti Liu; Olexandr Dybkov; Cindy L Will; Klaus Hartmuth; Henning Urlaub; Berthold Kastner; Holger Stark; Reinhard Lührmann

doi:10.1038/nature21079

Cryo-EM structure of a human spliceosome activated for step 2 of splicing

Nature. 2017 Feb 16;542(7641):318-323. doi: 10.1038/nature21079. Epub 2017 Jan 11.

Authors

Affiliations

¹ Department of Structural Dynamics, MPI for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany.
² Department of Cellular Biochemistry, MPI for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany.
³ Bioanalytical Mass Spectrometry, MPI for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany.
⁴ Bioanalytics Group, Institute for Clinical Chemistry, University Medical Centre Göttingen, Robert-Koch-Straße 40, D-37075 Göttingen, Germany.

PMID: 28076346
DOI: 10.1038/nature21079

Abstract

Spliceosome rearrangements facilitated by RNA helicase PRP16 before catalytic step two of splicing are poorly understood. Here we report a 3D cryo-electron microscopy structure of the human spliceosomal C complex stalled directly after PRP16 action (C*). The architecture of the catalytic U2-U6 ribonucleoprotein (RNP) core of the human C* spliceosome is very similar to that of the yeast pre-Prp16 C complex. However, in C* the branched intron region is separated from the catalytic centre by approximately 20 Å, and its position close to the U6 small nuclear RNA ACAGA box is stabilized by interactions with the PRP8 RNase H-like and PRP17 WD40 domains. RNA helicase PRP22 is located about 100 Å from the catalytic centre, suggesting that it destabilizes the spliced mRNA after step two from a distance. Comparison of the structure of the yeast C and human C* complexes reveals numerous RNP rearrangements that are likely to be facilitated by PRP16, including a large-scale movement of the U2 small nuclear RNP.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Adenosine / metabolism
Base Sequence
Biocatalysis
Cell Cycle Proteins / chemistry
Cell Cycle Proteins / metabolism
Cell Cycle Proteins / ultrastructure
Cryoelectron Microscopy*
DEAD-box RNA Helicases / chemistry
DEAD-box RNA Helicases / metabolism
DEAD-box RNA Helicases / ultrastructure
Exons / genetics
Humans
Introns / genetics
Models, Molecular
Movement
Protein Domains
RNA Splicing Factors / chemistry
RNA Splicing Factors / metabolism
RNA Splicing Factors / ultrastructure
RNA Splicing*
RNA Stability
RNA, Messenger / chemistry
RNA, Messenger / genetics
RNA, Messenger / metabolism
RNA-Binding Proteins / chemistry
RNA-Binding Proteins / metabolism
RNA-Binding Proteins / ultrastructure
Ribonuclease H / chemistry
Ribonuclease H / metabolism
Ribonucleoproteins, Small Nuclear / chemistry
Ribonucleoproteins, Small Nuclear / metabolism
Ribonucleoproteins, Small Nuclear / ultrastructure
Saccharomyces cerevisiae / chemistry
Saccharomyces cerevisiae / enzymology
Spliceosomes / chemistry
Spliceosomes / metabolism*
Spliceosomes / ultrastructure*

Substances

CDC40 protein, human
Cell Cycle Proteins
PRPF8 protein, human
RNA Splicing Factors
RNA, Messenger
RNA-Binding Proteins
Ribonucleoproteins, Small Nuclear
Ribonuclease H
DEAD-box RNA Helicases
DHX8 protein, human
Adenosine