Spliceosomal Sm core assembly: AlphaFold 3 predicted structure and phosphorylation-dependent regulation of the human 6S complex - Research Article

Sep 29, 2026

Uridine-rich small nuclear ribonucleoproteins (U snRNPs) form through a coordinated, multi-step chaperone-assisted pathway, yet regulatory mechanisms controlling U snRNP assembly remain incomplete. This study applies AlphaFold 3 to model the human 6S intermediate complex built from full-length pICln and SmD1/D2/E/F/G. Integrating computational modeling with biochemical evidence, results support a phosphorylation-dependent control of the pICln–SmG interface that enables downstream assembly and ULK1-driven serine phosphorylation to weaken interactions and favor ring opening, enabling targeted experimental validation.

LanguageEnglish

CategoryResearch & Report

FormatPDF

Pages10

Reading Time25 min

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Keywords

Abstract

1. Introduction

Computational and Structural Biotechnology Journal 31 (2026) 51–60 Contents lists available at ScienceDirect Computational and Structural Biotechnology Journal journal [homepage:](homepage: www.elsevier.com/locate/csbj)[ www.elsevier.com/locate/csbj](homepage: www.elsevier.com/locate/csbj) | Research Article
Spliceosomal Sm core assembly: AlphaFold 3 predicted structure and phosphorylation-dependent regulation of the human 6S complex | | | | | --- | --- | --- | --- | | Matthias Grimmler a,b,1 , Marco Reinhart c,1 , Sebastian Alers d , Christoph Peter e,*
a Institute for Biomolecular Research, Hochschule Fresenius, University of Applied Sciences, Idstein, Germany b DiaServe Laboratories GmbH, Iffeldorf, Germany
c GfA GmbH, Pfronten, Germany
d DiaSys Diagnostic Systems GmbH, Holzheim, Germany
e Institute of Molecular Medicine I, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany | | | | | A R T I C L E I N F O | | A B S T R A C T | | | Keywords: Spliceosome U snRNP assembly CLNS1A
ULK1
AlphaFold
Protein structure prediction | | The in vivo assembly of uridine-rich small nuclear ribonucleoproteins (U snRNPs), the central catalytic components of the spliceosome, is a highly organised, multi-step process orchestrated by several multi-protein complexes. Structural analyses have provided valuable insights into their overall architecture. However, critical information on the regulation of U snRNP assembly is still lacking. In this study, we used AlphaFold 3 to model the human 6S intermediate complex consisting of full-length pICln and five Sm proteins SmD1/D2/E/F/G. The available crystal structure used truncated non-vertebrate proteins, omitting the highly flexible C-terminal segments to permit crystallisation. However, the C-terminus of pICln has since been recognised as regulatory region, making full-length computational models an appropriate way to elucidate its structural and functional roles. By integrating modelling with biochemical data from previous studies, our results support a model in which the phosphorylation-dependent regulation of the pICln–SmG interface facilitates downstream assembly steps invertebrates, including the regulated displacement of pICln by the SmD3/B dimer. According to this model, ULK1-dependent serine phosphorylation in the C-terminal α-helix of pICln may abrogate the secondary structure and weakens its interaction with SmG, favouring ring opening. This complementary in silico approach elucidates the roles of regulatory regions in pICln that were previously inaccessible to crystallographic analysis and provides a framework for targeted experimental validation. | | 1. Introduction Pre-mRNA splicing is catalysed by the spliceosome, a large ribonucleoprotein complex in which uridine-rich small nuclear ribonucleoproteins (U snRNPs) provide splice-site recognition and, together with UsnRNAs, form the RNA-based catalytic core [1,2]. A key step in U snRNP biogenesis is the formation of a heptameric ring, the Sm core, comprising seven Sm proteins (SmB, D1, D2, D3, E, F, and G) [3,4]. Although Sm proteins and U snRNAs assemble spontaneously into functional U snRNPs in vitro, their formation in vivo is channelled through a multi-step, chaperone-assisted pathway [5–8]. The chaperone pICln participates in two assembly intermediates: the pICln–D3/B complex and the ring-shaped hetero-hexameric 6S complex containing pICln and SmD1/D2/E/F/G. In both intermediates, pICln prevents premature or incorrect assembly steps and pre-organises the Sm proteins into the order required for the mature heptameric Sm core [9–11]. Notably, pICln is essential for U snRNP assembly even in unicellular fission yeast [12]. The SMN complex, comprising SMN, Gemin2–8 and Unrip, then receives the Sm proteins from both the 6S and pICln–D3/B intermediate and assembles them onto the snRNA [7,9,10,13–15]. The precise mechanism by which pICln is displaced from the SmD1/ D2/E/F/

FAQs

What complex does the study model using AlphaFold 3?

The study models the human 6S intermediate complex composed of full-length pICln and five Sm proteins (SmD1/D2/E/F/G).

Why is a full-length computational model important for pICln in this work?

The only available experimental 6S structure used truncated non-vertebrate proteins that omitted flexible C-terminal segments, which are now recognized as regulatory; modeling full-length pICln helps clarify structural and functional roles.

How does ULK1 phosphorylation influence the pICln–SmG interaction and 6S structure?

ULK1-dependent serine phosphorylation in pICln’s C-terminal α-helix is proposed to disrupt secondary structure, weaken the pICln–SmG interaction, and favor a transition from a closed compact ring to an open, elongated state.

Sep 29, 2026

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