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  • 1
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    Crystal structure of Prp8 reveals active site cavity of the spliceosome (2013)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2013-01-29
    Description: The active centre of the spliceosome consists of an intricate network formed by U5, U2 and U6 small nuclear RNAs, and a pre-messenger-RNA substrate. Prp8, a component of the U5 small nuclear ribonucleoprotein particle, crosslinks extensively with this RNA catalytic core. Here we present the crystal structure of yeast Prp8 (residues 885-2413) in complex with Aar2, a U5 small nuclear ribonucleoprotein particle assembly factor. The structure reveals tightly associated domains of Prp8 resembling a bacterial group II intron reverse transcriptase and a type II restriction endonuclease. Suppressors of splice-site mutations, and an intron branch-point crosslink, map to a large cavity formed by the reverse transcriptase thumb, and the endonuclease-like and RNaseH-like domains. This cavity is large enough to accommodate the catalytic core of group II intron RNA. The structure provides crucial insights into the architecture of the spliceosome active site, and reinforces the notion that nuclear pre-mRNA splicing and group II intron splicing have a common origin.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3672837/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3672837/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Galej, Wojciech P -- Oubridge, Chris -- Newman, Andrew J -- Nagai, Kiyoshi -- MC_U105184330/Medical Research Council/United Kingdom -- U.1051.04.016(78933)/Medical Research Council/United Kingdom -- Medical Research Council/United Kingdom -- England -- Nature. 2013 Jan 31;493(7434):638-43. doi: 10.1038/nature11843. Epub 2013 Jan 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23354046" target="_blank"〉PubMed〈/a〉
    Keywords: Catalytic Domain ; *Models, Molecular ; Nuclear Proteins/chemistry/metabolism ; Protein Structure, Tertiary ; Ribonucleoprotein, U4-U6 Small Nuclear/*chemistry/genetics ; Ribonucleoprotein, U5 Small Nuclear/*chemistry/genetics ; Saccharomyces cerevisiae/*chemistry/genetics ; Saccharomyces cerevisiae Proteins/*chemistry/genetics/metabolism ; Spliceosomes/*chemistry
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 2
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    Cryo-EM structure of the yeast U4/U6.U5 tri-snRNP at 3.7 A resolution (2016)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2016-02-02
    Description: U4/U6.U5 tri-snRNP represents a substantial part of the spliceosome before activation. A cryo-electron microscopy structure of Saccharomyces cerevisiae U4/U6.U5 tri-snRNP at 3.7 A resolution led to an essentially complete atomic model comprising 30 proteins plus U4/U6 and U5 small nuclear RNAs (snRNAs). The structure reveals striking interweaving interactions of the protein and RNA components, including extended polypeptides penetrating into subunit interfaces. The invariant ACAGAGA sequence of U6 snRNA, which base-pairs with the 5'-splice site during catalytic activation, forms a hairpin stabilized by Dib1 and Prp8 while the adjacent nucleotides interact with the exon binding loop 1 of U5 snRNA. Snu114 harbours GTP, but its putative catalytic histidine is held away from the gamma-phosphate by hydrogen bonding to a tyrosine in the amino-terminal domain of Prp8. Mutation of this histidine to alanine has no detectable effect on yeast growth. The structure provides important new insights into the spliceosome activation process leading to the formation of the catalytic centre.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4762201/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4762201/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nguyen, Thi Hoang Duong -- Galej, Wojciech P -- Bai, Xiao-chen -- Oubridge, Chris -- Newman, Andrew J -- Scheres, Sjors H W -- Nagai, Kiyoshi -- MC_U105184330/Medical Research Council/United Kingdom -- MC_UP_A025_1013/Medical Research Council/United Kingdom -- England -- Nature. 2016 Feb 18;530(7590):298-302. doi: 10.1038/nature16940. Epub 2016 Feb 1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26829225" target="_blank"〉PubMed〈/a〉
    Keywords: Base Pairing ; Catalytic Domain ; *Cryoelectron Microscopy ; DNA Helicases/metabolism ; Exons/genetics ; Guanosine Triphosphate/metabolism ; Hydrogen Bonding ; Models, Molecular ; Nucleic Acid Conformation ; RNA Splice Sites ; RNA, Small Nuclear/chemistry/genetics/metabolism ; Ribonucleoprotein, U4-U6 Small Nuclear/chemistry/metabolism ; Ribonucleoprotein, U5 Small Nuclear/chemistry/metabolism ; Ribonucleoproteins, Small Nuclear/chemistry/genetics/metabolism/*ultrastructure ; Saccharomyces cerevisiae/chemistry/genetics/growth & development/*ultrastructure ; Saccharomyces cerevisiae Proteins/chemistry/genetics/metabolism/*ultrastructure ; Spliceosomes/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 3
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    The architecture of the spliceosomal U4/U6.U5 tri-snRNP (2015)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2015-06-25
    Description: U4/U6.U5 tri-snRNP is a 1.5-megadalton pre-assembled spliceosomal complex comprising U5 small nuclear RNA (snRNA), extensively base-paired U4/U6 snRNAs and more than 30 proteins, including the key components Prp8, Brr2 and Snu114. The tri-snRNP combines with a precursor messenger RNA substrate bound to U1 and U2 small nuclear ribonucleoprotein particles (snRNPs), and transforms into a catalytically active spliceosome after extensive compositional and conformational changes triggered by unwinding of the U4 and U6 (U4/U6) snRNAs. Here we use cryo-electron microscopy single-particle reconstruction of Saccharomyces cerevisiae tri-snRNP at 5.9 A resolution to reveal the essentially complete organization of its RNA and protein components. The single-stranded region of U4 snRNA between its 3' stem-loop and the U4/U6 snRNA stem I is loaded into the Brr2 helicase active site ready for unwinding. Snu114 and the amino-terminal domain of Prp8 position U5 snRNA to insert its loop I, which aligns the exons for splicing, into the Prp8 active site cavity. The structure provides crucial insights into the activation process and the active site of the spliceosome.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4536768/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4536768/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nguyen, Thi Hoang Duong -- Galej, Wojciech P -- Bai, Xiao-chen -- Savva, Christos G -- Newman, Andrew J -- Scheres, Sjors H W -- Nagai, Kiyoshi -- MC_U105184330/Medical Research Council/United Kingdom -- MC_UP_A025_1013/Medical Research Council/United Kingdom -- England -- Nature. 2015 Jul 2;523(7558):47-52. doi: 10.1038/nature14548. Epub 2015 Jun 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26106855" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Cryoelectron Microscopy ; *Models, Molecular ; Protein Structure, Quaternary ; RNA Helicases/chemistry/metabolism ; Ribonucleoprotein, U4-U6 Small Nuclear/*chemistry/metabolism ; Ribonucleoprotein, U5 Small Nuclear/chemistry/metabolism ; Saccharomyces cerevisiae/*chemistry/metabolism ; Saccharomyces cerevisiae Proteins/chemistry/metabolism ; Spliceosomes/chemistry/*physiology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 4
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    Postcatalytic spliceosome structure reveals mechanism of 3'-splice site selection (2017)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2017-12-08
    Description: Introns are removed from eukaryotic messenger RNA precursors by the spliceosome in two transesterification reactions—branching and exon ligation. The mechanism of 3'–splice site recognition during exon ligation has remained unclear. Here we present the 3.7-angstrom cryo–electron microscopy structure of the yeast P-complex spliceosome immediately after exon ligation. The 3'–splice site AG dinucleotide is recognized through non–Watson-Crick pairing with the 5' splice site and the branch-point adenosine. After the branching reaction, protein factors work together to remodel the spliceosome and stabilize a conformation competent for 3'–splice site docking, thereby promoting exon ligation. The structure accounts for the strict conservation of the GU and AG dinucleotides at the 5' and 3' ends of introns and provides insight into the catalytic mechanism of exon ligation.
    Keywords: Biochemistry, Molecular Biology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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