8QPK

Cryo-EM Structure of Pre-B+5'ss Complex (core part)

Summary for 8QPK

• Entry DOI: 10.2210/pdb8qpk/pdb
• EMDB information: 18555
• Descriptor: Probable ATP-dependent RNA helicase DDX23, U4 snRNA, U4/U6.U5 small nuclear ribonucleoprotein 27 kDa protein, ... (17 entities in total)
• Functional Keywords: spliceosome, splicing
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 16
• Total formula weight: 1339601.61

Authors

Zhang, Z.,Kumar, V.,Dybkov, O.,Will, C.L.,Zhong, J.,Ludwig, S.,Urlaub, H.,Kastner, B.,Stark, H.,Luehrmann, R. (deposition date: 2023-10-02, release date: 2024-05-22, Last modification date: 2024-07-10)

Primary citation

Zhang, Z.,Kumar, V.,Dybkov, O.,Will, C.L.,Zhong, J.,Ludwig, S.E.J.,Urlaub, H.,Kastner, B.,Stark, H.,Luhrmann, R.
Structural insights into the cross-exon to cross-intron spliceosome switch.
Nature, 630:1012-1019, 2024

PubMed Abstract: Early spliceosome assembly can occur through an intron-defined pathway, whereby U1 and U2 small nuclear ribonucleoprotein particles (snRNPs) assemble across the intron. Alternatively, it can occur through an exon-defined pathway, whereby U2 binds the branch site located upstream of the defined exon and U1 snRNP interacts with the 5' splice site located directly downstream of it. The U4/U6.U5 tri-snRNP subsequently binds to produce a cross-intron (CI) or cross-exon (CE) pre-B complex, which is then converted to the spliceosomal B complex. Exon definition promotes the splicing of upstream introns and plays a key part in alternative splicing regulation. However, the three-dimensional structure of exon-defined spliceosomal complexes and the molecular mechanism of the conversion from a CE-organized to a CI-organized spliceosome, a pre-requisite for splicing catalysis, remain poorly understood. Here cryo-electron microscopy analyses of human CE pre-B complex and B-like complexes reveal extensive structural similarities with their CI counterparts. The results indicate that the CE and CI spliceosome assembly pathways converge already at the pre-B stage. Add-back experiments using purified CE pre-B complexes, coupled with cryo-electron microscopy, elucidate the order of the extensive remodelling events that accompany the formation of B complexes and B-like complexes. The molecular triggers and roles of B-specific proteins in these rearrangements are also identified. We show that CE pre-B complexes can productively bind in trans to a U1 snRNP-bound 5' splice site. Together, our studies provide new mechanistic insights into the CE to CI switch during spliceosome assembly and its effect on pre-mRNA splice site pairing at this stage.

PubMed: 38778104
DOI: 10.1038/s41586-024-07458-1

Experimental method

ELECTRON MICROSCOPY (4.2 Å)