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Structure paper

TitleThe tumour suppressor RBM5 activates the helicase DHX15 to regulate splicing.
Journal, issue, pagesbioRxiv, Year 2026
Publish dateMar 27, 2026
AuthorsShiheng Liu / Tiantian Su / Jeffrey Huang / Chia-Ho Lin / Douglas L Black / Andrey Damianov / Z Hong Zhou
PubMed AbstractPre-mRNA splicing determines the expressed proteome and is frequently dysregulated in cancer. The tumour-suppressor RBM5 controls an exon network regulating apoptosis, yet its molecular mechanism is ...Pre-mRNA splicing determines the expressed proteome and is frequently dysregulated in cancer. The tumour-suppressor RBM5 controls an exon network regulating apoptosis, yet its molecular mechanism is elusive. Using in vivo spliceosome capture and cryogenic electron microscopy, we determined structures of precatalytic spliceosomes arrested by RBM5 immediately after U2 snRNP branchpoint recognition. Despite intron diversity, the U2-pre-mRNA duplex, branchpoint adenine, and downstream polypyrimidine tract are well-resolved. RBM5 binds the outer SF3B1 HEAT surface and performs dual functions: First, its helix-loop-helix motif and upstream zinc-finger domain sterically block tri-snRNP and Prp8 docking and prevent progression to pre-B and B complexes; Second, its G-patch activates DHX15 and places this DExH-box helicase on the pre-mRNA as it exits SF3B1, poised for branch helix unwinding. DHX15 binding to SF3B1 is facilitated by U2SURP/SR140, which engages SF3B1 near RBM5's helix-loop-helix. Functional assays confirm that disruption of the RBM5 interfaces with either DHX15 or SF3B1 inhibit exon repression. Mutations at these regulatory interfaces are common in cancer genomes and predicted to disrupt its regulation of apoptotic isoforms. Thus, RBM5 acts as a dual-action spliceosome gatekeeper that couples helicase activation with physical stalling to enforce tumour-suppressive alternative splicing programmes.
External linksbioRxiv / PubMed:41929118 / PubMed Central
MethodsEM (single particle)
Resolution3.26 - 3.94 Å
Structure data

74082

9ze0

EMDB-74082, PDB-9ze0:
Cryo-EM structure of the endogenous U2/branchpoint spliceosomal complex (Proximal DHX15 state)
Method: EM (single particle) / Resolution: 3.43 Å

74089

9ze2

EMDB-74089, PDB-9ze2:
Cryo-EM structure of the endogenous U2/branchpoint spliceosomal complex (core)
Method: EM (single particle) / Resolution: 3.26 Å

74090

9ze3

EMDB-74090, PDB-9ze3:
Cryo-EM structure of the endogenous U2/branchpoint spliceosomal complex (Distal DHX15 state)
Method: EM (single particle) / Resolution: 3.93 Å

74099

9zec

EMDB-74099, PDB-9zec:
Cryo-EM structure of the endogenous U2/branchpoint spliceosomal complex (SF3A state 1)
Method: EM (single particle) / Resolution: 3.61 Å

74100

9zed

EMDB-74100, PDB-9zed:
Cryo-EM structure of the endogenous U2/branchpoint spliceosomal complex (SF3A state 2)
Method: EM (single particle) / Resolution: 3.94 Å

Chemicals

ChemComp-ZN:
Unknown entry

Source
  • homo sapiens (human)
KeywordsSPLICING / spliceosome / tumor suppressor / helicase / DHX15 / RBM5 / SR140 / prespliceosomal A complex

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