Strategies for the structural analysis of multi-protein complexes: Lessons from the 3D-Repertoire project

Collinet, Bruno; Friberg, Anders; Brooks, Mark A.; Elzen, T van de; Henriot, Véronique; Dziembowski, Andrzej; Graille, Marc; Durand, Dominique; Leulliot, Nicolas; Andre, C Saint; Lazar, Noureddine; Sattler, Michael; Séraphin, Bertrand; Tilbeurgh, Herman van

doi:10.1016/j.jsb.2011.03.018

Cited by 17 publications

(20 citation statements)

References 58 publications

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“…In agreement with previous studies 15,16 , c Bud13p bound to monomeric c Snu17p with nanomolar affinity (Table 1). Moreover, c Bud13p bound to a preassembled c Snu17p-c Pml1p dimer with similar affinity ( Table 1).…”

Section: Res Assembly Is Highly Cooperativesupporting

confidence: 92%

“…Sequence homology of Bud13p to ligands that bind to U2AF-homology motifs of RRM domains suggested that Bud13p interacts with Snu17p according to canonical UHM-ULM interactions (Fig. 6b,d) 13,15,16,[18][19][20][21][22] . However, the three-dimensional structure of the RES core complex demonstrated a distinct interaction mode unlike that of UHM and ULM (Fig.…”

Section: Discussionmentioning

confidence: 99%

“…Snu17p binds with nanomolar affinity to the 266-residue (30.5-kDa), natively disordered protein Bud13p 15 . The interaction has been postulated to involve a C-terminal UHM-ligand motif (ULM) in Bud13p that interacts with a U2AF-homology motif (UHM) in the RRM domain of Snu17p 13,15,16 . The only other identified domain encompasses a stretch of lysine residues at the N terminus of Bud13p.…”

Section: 1 a R T I C L E Smentioning

confidence: 99%

“…The remainder of Pml1p folds as a forkhead-associated domain 13,15,17 , which could potentially bind phosphopeptides 17 . Biochemical evidence has suggested that Snu17p acts as the central binding platform, which interacts with disordered parts of Bud13p and Pml1p 13,15,16 . The precise molecular architecture of the RES complex, however, has been elusive, and its RNA binding capabilities have remained unexplored.…”

Section: 1 a R T I C L E Smentioning

confidence: 99%

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Cooperative structure of the heterotrimeric pre-mRNA retention and splicing complex

Wysoczanski

Schneider

Munari

et al. 2014

Nat Struct Mol Biol

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1 1 a r t i c l e sSplicing entails the removal of introns from pre-mRNAs to generate exon-only mRNA, which is exported out of the nucleus for translation 1 . The splicing process is driven and controlled by a large and dynamic RNA-protein complex, the spliceosome 1,2 . The composition and structure of the spliceosome undergoes multiple rearrangements during a splicing reaction, in which a set of distinct structural and compositional states, designated as E, A, B act , B* and C complexes, can be defined 1 . As part of this process, small nuclear ribonucleoprotein (snRNP) particles and non-snRNP splice factors are recruited and released 1,2 . Although the organization of snRNP components of the spliceosome has received considerable attention in recent years, very little is known about the assembly, structure and dynamics of non-snRNP multimeric complexes.The non-snRNP RES complex is present in humans and yeast 3,4 . Deletion of RES genes slows splicing and leads to pre-mRNA leakage into the cytoplasm 3-5 . Distinct introns exhibit RES-dependent splicing 5-9 , as do pre-mRNAs encoding proteins functioning in RNA-nucleotide metabolism 8,10 . Components of the RES complex are found in B and C complexes of the spliceosome, in which RES can interact with U2 snRNP 4,11,12 . In yeast, the RES complex is composed of three proteins, snRNP-associated protein 17 (Snu17p, also known as Ist3p), pre-mRNA-leakage protein 1 (Pml1p) and bud siteselection protein 13 (Bud13p) 3,4 . Snu17p and Bud13p have been implicated directly in splicing 3,5,13 , whereas Pml1p has been linked to the retention of unspliced pre-mRNA in the nucleus 3,5 . Caenorhabditis elegans Bud13p is involved in embryogenesis 14 .Sequence analysis has indicated that Snu17p is a 148-residue (17.1-kDa) noncanonical member of the RRM family of proteins with a long C-terminal part, which exhibits low sequence similarity to published RRM structures 4 . Snu17p binds with nanomolar affinity to the 266-residue (30.5-kDa), natively disordered protein Bud13p 15 . The interaction has been postulated to involve a C-terminal UHM-ligand motif (ULM) in Bud13p that interacts with a U2AF-homology motif (UHM) in the RRM domain of Snu17p 13,15,16 . The only other identified domain encompasses a stretch of lysine residues at the N terminus of Bud13p. Binding of the third component, the 204-residue (23.4-kDa) Pml1p, occurs through its 50 N-terminal disordered residues. The remainder of Pml1p folds as a forkhead-associated domain 13,15,17 , which could potentially bind phosphopeptides 17 . Biochemical evidence has suggested that Snu17p acts as the central binding platform, which interacts with disordered parts of Bud13p and Pml1p 13,15,16 . The precise molecular architecture of the RES complex, however, has been elusive, and its RNA binding capabilities have remained unexplored.Here we solved the three-dimensional structure of the core of the RES complex and demonstrated that its assembly is driven by cooperativity that increases the binding affinity of the components of the complex ...

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Section: Res Assembly Is Highly Cooperativesupporting

confidence: 92%

Section: Discussionmentioning

confidence: 99%

Section: 1 a R T I C L E Smentioning

confidence: 99%

Section: 1 a R T I C L E Smentioning

confidence: 99%

See 2 more Smart Citations

Cooperative structure of the heterotrimeric pre-mRNA retention and splicing complex

Wysoczanski

Schneider

Munari

et al. 2014

Nat Struct Mol Biol

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“…40,49 Confirmation that the KEOPS/EKC complex was responsible for t 6 A formation came with in vitro reconstitution experiments. It was shown that both the KEOPS/EKC complex from Pyrococcus abyssi (Kae1, Bud32, Pcc1, and Cgi121), reconstituted from the individual genes expressed in E. coli, as well as the S. cerevisiae KEOPS complex (Kae1, Bud32, Pcc1, Cgi121, and Gon7), genes expressed in E. coli as a synthetic operon, 50 can form t 6 A in vitro, when combined with Sua5 from yeast or Archaea.…”

Section: Archaea and Eukaryamentioning

confidence: 99%

Diversity of the biosynthesis pathway for threonylcarbamoyladenosine (t⁶A), a universal modification of tRNA

2014

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Current methods in structural proteomics and its applications in biological sciences

et al. 2011

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A broad working definition of structural proteomics (SP) is that it is the process of the high-throughput characterization of the three-dimensional structures of biological macromolecules. Recently, the process for protein structure determination has become highly automated and SP platforms have been established around the globe, utilizing X-ray crystallography as a tool. Although protein structures often provide clues about the biological function of a target, once the three-dimensional structures have been determined, bioinformatics and proteomics-driven strategies can be employed to derive their biological activities and physiological roles. This article reviews the current status of SP methods for the structure determination pipeline, including target selection, isolation, expression, purification, crystallization, diffraction data collection, structure solution, refinement and functional annotation.

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Strategies for the structural analysis of multi-protein complexes: Lessons from the 3D-Repertoire project

Cited by 17 publications

References 58 publications

Cooperative structure of the heterotrimeric pre-mRNA retention and splicing complex

Cooperative structure of the heterotrimeric pre-mRNA retention and splicing complex

Diversity of the biosynthesis pathway for threonylcarbamoyladenosine (t⁶A), a universal modification of tRNA

Current methods in structural proteomics and its applications in biological sciences

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Strategies for the structural analysis of multi-protein complexes: Lessons from the 3D-Repertoire project

Cited by 17 publications

References 58 publications

Cooperative structure of the heterotrimeric pre-mRNA retention and splicing complex

Cooperative structure of the heterotrimeric pre-mRNA retention and splicing complex

Diversity of the biosynthesis pathway for threonylcarbamoyladenosine (t6A), a universal modification of tRNA

Current methods in structural proteomics and its applications in biological sciences

Contact Info

Product

Resources

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Diversity of the biosynthesis pathway for threonylcarbamoyladenosine (t⁶A), a universal modification of tRNA