5MPS

Structure of a spliceosome remodeled for exon ligation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.85 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of a spliceosome remodelled for exon ligation.

Fica, S.M.Oubridge, C.Galej, W.P.Wilkinson, M.E.Bai, X.C.Newman, A.J.Nagai, K.

(2017) Nature 542: 377-380

  • DOI: 10.1038/nature21078
  • Primary Citation of Related Structures:  

  • PubMed 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 w ...

    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.


    Related Citations: 
    • Cryo-EM structure of the spliceosome immediately after branching.
      Galej, W.P.,Wilkinson, M.E.,Fica, S.M.,Oubridge, C.,Newman, A.J.,Nagai, K.
      (2016) Nature 537: 197
    • The architecture of the spliceosomal U4/U6.U5 tri-snRNP.
      Nguyen, T.H.,Galej, W.P.,Bai, X.C.,Savva, C.G.,Newman, A.J.,Scheres, S.H.,Nagai, K.
      (2015) Nature 523: 47
    • Cryo-EM structure of the yeast U4/U6.U5 tri-snRNP at 3.7 A resolution.
      Nguyen, T.H.,Galej, W.P.,Bai, X.C.,Oubridge, C.,Newman, A.J.,Scheres, S.H.,Nagai, K.
      (2016) Nature 530: 298
    • Structural basis of pre-mRNA splicing.
      Hang, J.,Wan, R.,Yan, C.,Shi, Y.
      (2015) Science 349: 1191


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor 8
A
2413Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRP8 (DBF3, DNA39, RNA8, SLT21, USA2)
Find proteins for P33334 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P33334
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor SNU114
C
1008Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SNU114 (GIN10)
Find proteins for P36048 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P36048
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor CWC22
H
577Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CWC22
Find proteins for P53333 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: CWC22
Go to UniProtKB:  P53333
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor PRP46
J
451Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRP46 (CWC1, NTC50)
Find proteins for Q12417 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12417
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing protein 45
K
379Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRP45 (FUN20)
Find proteins for P28004 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P28004
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor BUD31
L
157Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: BUD31 (CWC14)
Find proteins for P25337 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: BUD31
Go to UniProtKB:  P25337
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor CWC2
M
339Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CWC2 (NTC40, SLC3)
Find proteins for Q12046 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12046
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor SLT11
N
364Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: ECM2 (SLT11)
Find proteins for P38241 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: ECM2
Go to UniProtKB:  P38241
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor CEF1
O
590Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CEF1 (NTC85)
Find proteins for Q03654 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q03654
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor CWC15
P
175Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CWC15
Find proteins for Q03772 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: CWC15
Go to UniProtKB:  Q03772
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor CWC21
R
135Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CWC21
Find proteins for Q03375 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q03375
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor CLF1
S
687Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CLF1 (NTC77, SYF3)
Find proteins for Q12309 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12309
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor SYF1
T
877Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SYF1 (NTC90)
Find proteins for Q04048 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q04048
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor 18
a
251Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRP18
Find proteins for P33411 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P33411
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor SLU7
c
382Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SLU7 (SLT17)
Find proteins for Q02775 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: SLU7
Go to UniProtKB:  Q02775
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing factor 17
o
455Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CDC40 (PRP17, SLU4, XRS2)
Find proteins for P40968 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: CDC40
Go to UniProtKB:  P40968
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Unknown
X
68N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor SYF2
y
215Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SYF2 (NTC31)
Find proteins for P53277 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: SYF2
Go to UniProtKB:  P53277
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein-associated protein B
b
196Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SMB1
Find proteins for P40018 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40018
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D3
d
101Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SMD3
Find proteins for P43321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P43321
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein E
e
94Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SME1
Find proteins for Q12330 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12330
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein F
f
86Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SMX3
Find proteins for P54999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P54999
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein G
g
77Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SMX2 (SNP2)
Find proteins for P40204 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40204
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D1
h
146Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SMD1
Find proteins for Q02260 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q02260
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D2
j
110Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SMD2
Find proteins for Q06217 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q06217
Entity ID: 1
MoleculeChainsLengthOrganism
Yeast UBC4 gene for ubiquitin-conjugating enzymeI95Saccharomyces cerevisiae
Entity ID: 2
MoleculeChainsLengthOrganism
UBC4 gene exonE20Saccharomyces cerevisiae
Entity ID: 3
MoleculeChainsLengthOrganism
U2 snRNA21175Saccharomyces cerevisiae
Entity ID: 4
MoleculeChainsLengthOrganism
Saccharomyces cerevisiae strain T.52_2H chromosome XII sequence6112Saccharomyces cerevisiae
Entity ID: 5
MoleculeChainsLengthOrganism
U5 snRNA5179Saccharomyces cerevisiae
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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Download CCD File 
6
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
I6P
Query on I6P

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A
INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE
MYO-INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
 Ligand Interaction
ZN
Query on ZN

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Download CCD File 
L, M, N
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GTP
Query on GTP

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Download CCD File 
C
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
6
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
T, X
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.85 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMC-U105184330
European Research CouncilAdG-693087-SPLICE3D
EMBO and Marie Sklodowska-Curie FellowshipRef. S.M.Fica

Revision History 

  • Version 1.0: 2017-01-18
    Type: Initial release
  • Version 1.1: 2017-03-01
    Type: Database references
  • Version 1.2: 2017-07-05
    Type: Data collection
  • Version 1.3: 2017-08-30
    Type: Author supporting evidence, Data collection