Structural model of the p14/SF3b155·branch duplex complex

Schellenberg, M.J.; Dul, E.L; MacMillan, Andrew M.

doi:10.1261/rna.2224411

Cited by 22 publications

(24 citation statements)

References 59 publications

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“…There seems to be flexibility in the choice of the BP adenosine, as either one of the two A residues present in the consensus BPS can be used as a BP, depending on the intron in question 52. BPS recognition is likely stabilized by proteins of the SF3b complex, which is present in both spliceosomes (Table 1), and is known to bind to the BPS in the major spliceosome, with the protein factor p14 shielding the BP adenosine from premature activation 39,53,54. U12‐type introns do not have PPTs, and U2AF is not required for the recognition of U12‐type introns 55.…”

Section: Spliceosome Assembly and Catalysismentioning

confidence: 99%

The significant other: splicing by the minor spliceosome

et al. 2012

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The removal of non-coding sequences, introns, from the mRNA precursors is an essential step in eukaryotic gene expression. U12-type introns are a minor subgroup of introns, distinct from the major or U2-type introns. U12-type introns are present in most eukaryotes but only account for less than 0.5% of all introns in any given genome. They are processed by a specific U12-dependent spliceosome, which is similar to, but distinct from, the major spliceosome. U12-type introns are spliced somewhat less efficiently than the major introns, and it is believed that this limits the expression of the genes containing such introns. Recent findings on the role of U12-dependent splicing in development and human disease have shown that it can also affect multiple cellular processes not directly related to the functions of the host genes of U12-type introns. At the same time, advances in understanding the regulation and phylogenetic distribution of the minor spliceosome are starting to shed light on how the U12-type introns and the minor spliceosome may have evolved. © 2012 John Wiley & Sons, Ltd.

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Section: Spliceosome Assembly and Catalysismentioning

confidence: 99%

The significant other: splicing by the minor spliceosome

et al. 2012

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“…Hence, we modeled the branch point duplex (BPD) containing U12 snRNA and pre-mRNA, including the BPA, using an available crystal structure of BPD (PDB ID: 1I9X) 84 and prior knowledge of U12 snRNA: pre-mRNA base pairing. 85 The information on the recognition of BPA by p14 was collated from multiple sources 9,30 and the p14-BPD complex structure was modeled using a restrained docking procedure (see Materials and Methods). Further, we found that the p14-BPD docked complex structures fitted snugly into the groove above p14 density surface, when fitted in the U11/U12 di-snRNP cryo-EM map.…”

Section: U12 Snrna and Branch Point Duplex Binding To Sf3b Open Formmentioning

confidence: 99%

“…8 It forms a dynamic and integral part of 4 intermediary complexes (A, B, B Ã and B act ). Previous studies have revealed various roles for SF3b complex including i) recognition of branch point adenosine 9 and promotion of stable interaction for U2 and U11/U12 di-snRNP to pre-mRNA, 10 ii) prevention of premature splicing 10 and iii) interaction with snRNAs and pre-mRNA. 11,12 The complex is made of 7 proteins, namely, p14, SF3b49, SF3b145, SF3b155, SF3b10, SF3b130 and SF3b14b.…”

Section: Introductionmentioning

confidence: 99%

“…[12][13][14] p14, an RRMdomain containing protein, has been shown to recognize the branch point adenosine (BPA) within the bulged branch point duplex (BPD) structure formed between pre-mRNA and branch point recognition sequence (BPRS) of U2/U12 snRNA. 9,15 This enables SF3b to present a temporary steric barrier to branch point sequence (BPS) prior to activation. 10 In addition, SF3b49 has been shown to interact with the stemloops at 5 0 end of U2 snRNA 11 and is also shown to be cross linked around the BPS along with the other components such as the SF3b145 and SF3b155.…”

Section: Introductionmentioning

confidence: 99%

“…29 Subsequently, NMR structures of the 2 RRM domains of SF3b49 (PDB ID: 1X5U and 1X5T; Structural genomics consortium) were also determined. For p14, both crystal (PDB ID: 2F9D, 3LQV) 9,30 and NMR structures (PDB ID: 2FHO) 31 became available along with the peptide component of SF3b155. To date, this is the only inter-molecular interaction, defined at atomic level, in the SF3b complex.…”

Section: Introductionmentioning

confidence: 99%

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Structural and mechanistic insights into human splicing factor SF3b complex derived using an integrated approach guided by the cryo-EM density maps

et al. 2016

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Pre-mRNA splicing in eukaryotes is performed by the spliceosome, a highly complex macromolecular machine. SF3b is a multi-protein complex which recognizes the branch point adenosine of pre-mRNA as part of a larger U2 snRNP or U11/U12 di-snRNP in the dynamic spliceosome machinery. Although a cryo-EM map is available for human SF3b complex, the structure and relative spatial arrangement of all components in the complex are not yet known. We have recognized folds of domains in various proteins in the assembly and generated comparative models. Using an integrative approach involving structural and other experimental data, guided by the available cryo-EM density map, we deciphered a pseudoatomic model of the closed form of SF3b which is found to be a "fuzzy complex" with highly flexible components and multiplicity of folds. Further, the model provides structural information for 5 proteins (SF3b10, SF3b155, SF3b145, SF3b130 and SF3b14b) and localization information for 4 proteins (SF3b10, SF3b145, SF3b130 and SF3b14b) in the assembly for the first time. Integration of this model with the available U11/U12 di-snRNP cryo-EM map enabled elucidation of an open form. This now provides new insights on the mechanistic features involved in the transition between closed and open forms pivoted by a hinge region in the SF3b155 protein that also harbors cancer causing mutations. Moreover, the open form guided model of the 5 0 end of U12 snRNA, which includes the branch point duplex, shows that the architecture of SF3b acts as a scaffold for U12 snRNA: pre-mRNA branch point duplex formation with potential implications for branch point adenosine recognition fidelity.

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