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TitleStructural insights into the cross-exon to cross-intron spliceosome switch.
Journal, issue, pagesNature, Year 2024
Publish dateMay 22, 2024
AuthorsZhenwei Zhang / Vinay Kumar / Olexandr Dybkov / Cindy L Will / Jiayun Zhong / Sebastian E J Ludwig / Henning Urlaub / Berthold Kastner / Holger Stark / Reinhard Lührmann /
PubMed AbstractEarly 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 ...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.
External linksNature / PubMed:38778104
MethodsEM (single particle)
Resolution3.1 - 9.6 Å
Structure data

EMDB-18542, PDB-8qoz:
Cryo-EM Structure of Pre-B+5'ss+ATPgammaS Complex (core part)
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-18544, PDB-8qp8:
Cryo-EM Structure of Pre-B Complex (core part)
Method: EM (single particle) / Resolution: 3.5 Å

EMDB-18545, PDB-8qp9:
Cryo-EM Structure of Pre-B+AMPPNP Complex (core part)
Method: EM (single particle) / Resolution: 4.1 Å

EMDB-18546, PDB-8qpa:
Cryo-EM Structure of Pre-B+5'ssLNG Complex (core part)
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-18547, PDB-8qpb:
Cryo-EM Structure of Pre-B+ATP Complex (core part)
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-18548, PDB-8qpe:
Cryo-EM Structure of Pre-B-like Complex (core part)
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-18555, PDB-8qpk:
Cryo-EM Structure of Pre-B+5'ss Complex (core part)
Method: EM (single particle) / Resolution: 4.2 Å

EMDB-18718, PDB-8qxd:
Cryo-EM structure of the cross-exon pre-B complex
Method: EM (single particle) / Resolution: 9.6 Å

EMDB-18781, PDB-8qzs:
Cryo-EM structure of the cross-exon B-like complex
Method: EM (single particle) / Resolution: 4.1 Å

EMDB-18786, PDB-8r08:
Cryo-EM structure of the cross-exon pre-B+AMPPNP complex
Method: EM (single particle) / Resolution: 6.1 Å

EMDB-18787, PDB-8r09:
Cryo-EM structure of the cross-exon pre-B+5'ss+ATPgammaS complex
Method: EM (single particle) / Resolution: 4.3 Å

EMDB-18788, PDB-8r0a:
Cryo-EM structure of the cross-exon pre-B+5'ss complex
Method: EM (single particle) / Resolution: 5.8 Å

EMDB-18789, PDB-8r0b:
Cryo-EM structure of the cross-exon pre-B+ATP complex
Method: EM (single particle) / Resolution: 4.4 Å

EMDB-19349, PDB-8rm5:
Cryo-EM structure of the cross-exon pre-B+5'ssLNG+ATPyS complex
Method: EM (single particle) / Resolution: 6.9 Å

Chemicals

ChemComp-IHP:
INOSITOL HEXAKISPHOSPHATE / Phytic acid

Source
  • homo sapiens (human)
KeywordsSPLICING / spliceosome

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