Structure of a spliceosome remodelled for exon ligation

Sebastian M. Fica, Chris Oubridge, Wojciech P. Galej, Max E. Wilkinson, Xiao Chen Bai, Andrew J. Newman, Kiyoshi Nagai

Research output: Contribution to journalArticle

77 Citations (Scopus)

Abstract

The spliceosome excises introns from pre-mRNAs in two sequential transesterifications - branching and exon ligation - catalysed at a single catalytic metal site in U6 small nuclear RNA (snRNA). Recently reported structures of the spliceosomal C complex with the cleaved 5′ exon and lariat-3′-exon bound to the catalytic centre revealed that branching-specific factors such as Cwc25 lock the branch helix into position for nucleophilic attack of the branch adenosine at the 5′ splice site. Furthermore, the ATPase Prp16 is positioned to bind and translocate the intron downstream of the branch point to destabilize branching-specific factors and release the branch helix from the active site. Here we present, at 3.8 Å resolution, the cryo-electron microscopy structure of a Saccharomyces cerevisiae spliceosome stalled after Prp16-mediated remodelling but before exon ligation. While the U6 snRNA catalytic core remains firmly held in the active site cavity of Prp8 by proteins common to both steps, the branch helix has rotated by 75° compared to the C complex and is stabilized in a new position by Prp17, Cef1 and the reoriented Prp8 RNase H-like domain. This rotation of the branch helix removes the branch adenosine from the catalytic core, creates a space for 3′ exon docking, and restructures the pairing of the 5′ splice site with the U6 snRNA ACAGAGA region. Slu7 and Prp18, which promote exon ligation, bind together to the Prp8 RNase H-like domain. The ATPase Prp22, bound to Prp8 in place of Prp16, could interact with the 3′ exon, suggesting a possible basis for mRNA release after exon ligation. Together with the structure of the C complex, our structure of the C∗ complex reveals the two major conformations of the spliceosome during the catalytic stages of splicing.

Original languageEnglish (US)
Pages (from-to)377-380
Number of pages4
JournalNature
Volume542
Issue number7641
DOIs
StatePublished - Feb 16 2017

Fingerprint

Spliceosomes
Ligation
Exons
Catalytic Domain
Ribonuclease H
RNA Splice Sites
Adenosine
Introns
Adenosine Triphosphatases
Cryoelectron Microscopy
RNA Precursors
Saccharomyces cerevisiae
Metals
Messenger RNA

ASJC Scopus subject areas

  • General

Cite this

Fica, S. M., Oubridge, C., Galej, W. P., Wilkinson, M. E., Bai, X. C., Newman, A. J., & Nagai, K. (2017). Structure of a spliceosome remodelled for exon ligation. Nature, 542(7641), 377-380. https://doi.org/10.1038/nature21078

Structure of a spliceosome remodelled for exon ligation. / Fica, Sebastian M.; Oubridge, Chris; Galej, Wojciech P.; Wilkinson, Max E.; Bai, Xiao Chen; Newman, Andrew J.; Nagai, Kiyoshi.

In: Nature, Vol. 542, No. 7641, 16.02.2017, p. 377-380.

Research output: Contribution to journalArticle

Fica, SM, Oubridge, C, Galej, WP, Wilkinson, ME, Bai, XC, Newman, AJ & Nagai, K 2017, 'Structure of a spliceosome remodelled for exon ligation', Nature, vol. 542, no. 7641, pp. 377-380. https://doi.org/10.1038/nature21078
Fica SM, Oubridge C, Galej WP, Wilkinson ME, Bai XC, Newman AJ et al. Structure of a spliceosome remodelled for exon ligation. Nature. 2017 Feb 16;542(7641):377-380. https://doi.org/10.1038/nature21078
Fica, Sebastian M. ; Oubridge, Chris ; Galej, Wojciech P. ; Wilkinson, Max E. ; Bai, Xiao Chen ; Newman, Andrew J. ; Nagai, Kiyoshi. / Structure of a spliceosome remodelled for exon ligation. In: Nature. 2017 ; Vol. 542, No. 7641. pp. 377-380.
@article{fefd46fcaac64966b1e7a0b05667f68e,
title = "Structure of a spliceosome remodelled for exon ligation",
abstract = "The spliceosome excises introns from pre-mRNAs in two sequential transesterifications - branching and exon ligation - catalysed at a single catalytic metal site in U6 small nuclear RNA (snRNA). Recently reported structures of the spliceosomal C complex with the cleaved 5′ exon and lariat-3′-exon bound to the catalytic centre revealed that branching-specific factors such as Cwc25 lock the branch helix into position for nucleophilic attack of the branch adenosine at the 5′ splice site. Furthermore, the ATPase Prp16 is positioned to bind and translocate the intron downstream of the branch point to destabilize branching-specific factors and release the branch helix from the active site. Here we present, at 3.8 {\AA} resolution, the cryo-electron microscopy structure of a Saccharomyces cerevisiae spliceosome stalled after Prp16-mediated remodelling but before exon ligation. While the U6 snRNA catalytic core remains firmly held in the active site cavity of Prp8 by proteins common to both steps, the branch helix has rotated by 75° compared to the C complex and is stabilized in a new position by Prp17, Cef1 and the reoriented Prp8 RNase H-like domain. This rotation of the branch helix removes the branch adenosine from the catalytic core, creates a space for 3′ exon docking, and restructures the pairing of the 5′ splice site with the U6 snRNA ACAGAGA region. Slu7 and Prp18, which promote exon ligation, bind together to the Prp8 RNase H-like domain. The ATPase Prp22, bound to Prp8 in place of Prp16, could interact with the 3′ exon, suggesting a possible basis for mRNA release after exon ligation. Together with the structure of the C complex, our structure of the C∗ complex reveals the two major conformations of the spliceosome during the catalytic stages of splicing.",
author = "Fica, {Sebastian M.} and Chris Oubridge and Galej, {Wojciech P.} and Wilkinson, {Max E.} and Bai, {Xiao Chen} and Newman, {Andrew J.} and Kiyoshi Nagai",
year = "2017",
month = "2",
day = "16",
doi = "10.1038/nature21078",
language = "English (US)",
volume = "542",
pages = "377--380",
journal = "Nature",
issn = "0028-0836",
publisher = "Nature Publishing Group",
number = "7641",

}

TY - JOUR

T1 - Structure of a spliceosome remodelled for exon ligation

AU - Fica, Sebastian M.

AU - Oubridge, Chris

AU - Galej, Wojciech P.

AU - Wilkinson, Max E.

AU - Bai, Xiao Chen

AU - Newman, Andrew J.

AU - Nagai, Kiyoshi

PY - 2017/2/16

Y1 - 2017/2/16

N2 - The spliceosome excises introns from pre-mRNAs in two sequential transesterifications - branching and exon ligation - catalysed at a single catalytic metal site in U6 small nuclear RNA (snRNA). Recently reported structures of the spliceosomal C complex with the cleaved 5′ exon and lariat-3′-exon bound to the catalytic centre revealed that branching-specific factors such as Cwc25 lock the branch helix into position for nucleophilic attack of the branch adenosine at the 5′ splice site. Furthermore, the ATPase Prp16 is positioned to bind and translocate the intron downstream of the branch point to destabilize branching-specific factors and release the branch helix from the active site. Here we present, at 3.8 Å resolution, the cryo-electron microscopy structure of a Saccharomyces cerevisiae spliceosome stalled after Prp16-mediated remodelling but before exon ligation. While the U6 snRNA catalytic core remains firmly held in the active site cavity of Prp8 by proteins common to both steps, the branch helix has rotated by 75° compared to the C complex and is stabilized in a new position by Prp17, Cef1 and the reoriented Prp8 RNase H-like domain. This rotation of the branch helix removes the branch adenosine from the catalytic core, creates a space for 3′ exon docking, and restructures the pairing of the 5′ splice site with the U6 snRNA ACAGAGA region. Slu7 and Prp18, which promote exon ligation, bind together to the Prp8 RNase H-like domain. The ATPase Prp22, bound to Prp8 in place of Prp16, could interact with the 3′ exon, suggesting a possible basis for mRNA release after exon ligation. Together with the structure of the C complex, our structure of the C∗ complex reveals the two major conformations of the spliceosome during the catalytic stages of splicing.

AB - The spliceosome excises introns from pre-mRNAs in two sequential transesterifications - branching and exon ligation - catalysed at a single catalytic metal site in U6 small nuclear RNA (snRNA). Recently reported structures of the spliceosomal C complex with the cleaved 5′ exon and lariat-3′-exon bound to the catalytic centre revealed that branching-specific factors such as Cwc25 lock the branch helix into position for nucleophilic attack of the branch adenosine at the 5′ splice site. Furthermore, the ATPase Prp16 is positioned to bind and translocate the intron downstream of the branch point to destabilize branching-specific factors and release the branch helix from the active site. Here we present, at 3.8 Å resolution, the cryo-electron microscopy structure of a Saccharomyces cerevisiae spliceosome stalled after Prp16-mediated remodelling but before exon ligation. While the U6 snRNA catalytic core remains firmly held in the active site cavity of Prp8 by proteins common to both steps, the branch helix has rotated by 75° compared to the C complex and is stabilized in a new position by Prp17, Cef1 and the reoriented Prp8 RNase H-like domain. This rotation of the branch helix removes the branch adenosine from the catalytic core, creates a space for 3′ exon docking, and restructures the pairing of the 5′ splice site with the U6 snRNA ACAGAGA region. Slu7 and Prp18, which promote exon ligation, bind together to the Prp8 RNase H-like domain. The ATPase Prp22, bound to Prp8 in place of Prp16, could interact with the 3′ exon, suggesting a possible basis for mRNA release after exon ligation. Together with the structure of the C complex, our structure of the C∗ complex reveals the two major conformations of the spliceosome during the catalytic stages of splicing.

UR - http://www.scopus.com/inward/record.url?scp=85016141734&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85016141734&partnerID=8YFLogxK

U2 - 10.1038/nature21078

DO - 10.1038/nature21078

M3 - Article

C2 - 28076345

AN - SCOPUS:85016141734

VL - 542

SP - 377

EP - 380

JO - Nature

JF - Nature

SN - 0028-0836

IS - 7641

ER -