9NB1

CRYO-EM STRUCTURE OF human U7 SNRNP WITH MUTANT LSM11 that disrupts contacts with CPSF73

Summary for 9NB1

• Entry DOI: 10.2210/pdb9nb1/pdb
• Related: 9N96 9NAF
• EMDB information: 49206
• Descriptor: Small nuclear ribonucleoprotein Sm D3, Small nuclear ribonucleoprotein-associated proteins B and B', U7 snRNA-associated Sm-like protein LSm11, ... (14 entities in total)
• Functional Keywords: 3' end processing, u7 snrnp, histone pre-mrna, rna binding protein, rna binding protein-rna complex, rna binding protein/rna
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 13
• Total formula weight: 423138.88

Authors

Desotell, A.,Tong, L. (deposition date: 2025-02-13, release date: 2026-01-21)

Primary citation

Desotell, A.,Marzluff, W.F.,Dominski, Z.,Tong, L.
An N-terminal helix of Lsm11 stabilizes CPSF73 in U7 snRNP for histone pre-mRNA 3'-end processing.
Nucleic Acids Res., 54:-, 2026

PubMed Abstract: The U7 snRNP (small nuclear ribonucleoprotein) is responsible for the 3'-end processing of replication-dependent histone messenger RNA precursors (pre-mRNAs). A helix in the Lsm11 N-terminal extension contacts the metallo-β-lactamase domain of the U7 snRNP endonuclease CPSF73. We mutated or deleted this helix and found that the mutant machineries had substantially reduced cleavage activity toward the pre-mRNA. Our cryo-electron microscopy (cryo-EM) studies indicated that the helix was important for helping to hold CPSF73 in its correct position for the cleavage reaction. We also reconstituted a wild-type U7 snRNP in complex with a methylated, noncleavable pre-mRNA. We observed that CPSF73 could achieve an open conformation independent of RNA binding to its active site. Finally, we found that a previously uninterpreted EM density for a small helix at the CPSF73-CPSF100 interface belonged to the C-terminal end of CstF77, copurified from insect cells and highly conserved among CstF77 homologs. This CstF77 binding site had a small effect on the cleavage activity of U7 snRNP. Overall, our studies have revealed the importance of the conserved helix in the Lsm11 N-terminal extension for U7 snRNP, provided structural evidence that CPSF73 can achieve an open, active conformation without RNA binding in its active site, and identified a previously unknown binding site for CstF77 in CPSF100.

PubMed: 41495886
DOI: 10.1093/nar/gkaf1442

Experimental method

ELECTRON MICROSCOPY (3.85 Å)