6G90

Prespliceosome structure provides insight into spliceosome assembly and regulation (map A2)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Prespliceosome structure provides insights into spliceosome assembly and regulation.

Plaschka, C.Lin, P.C.Charenton, C.Nagai, K.

(2018) Nature 559: 419-422

  • DOI: 10.1038/s41586-018-0323-8

  • PubMed Abstract: 
  • The spliceosome catalyses the excision of introns from pre-mRNA in two steps, branching and exon ligation, and is assembled from five small nuclear ribonucleoprotein particles (snRNPs; U1, U2, U4, U5, U6) and numerous non-snRNP factors <sup>1 </sup>. ...

    The spliceosome catalyses the excision of introns from pre-mRNA in two steps, branching and exon ligation, and is assembled from five small nuclear ribonucleoprotein particles (snRNPs; U1, U2, U4, U5, U6) and numerous non-snRNP factors 1 . For branching, the intron 5' splice site and the branch point sequence are selected and brought by the U1 and U2 snRNPs into the prespliceosome 1 , which is a focal point for regulation by alternative splicing factors 2 . The U4/U6.U5 tri-snRNP subsequently joins the prespliceosome to form the complete pre-catalytic spliceosome. Recent studies have revealed the structural basis of the branching and exon-ligation reactions 3 , however, the structural basis of the early events in spliceosome assembly remains poorly understood 4 . Here we report the cryo-electron microscopy structure of the yeast Saccharomyces cerevisiae prespliceosome at near-atomic resolution. The structure reveals an induced stabilization of the 5' splice site in the U1 snRNP, and provides structural insights into the functions of the human alternative splicing factors LUC7-like (yeast Luc7) and TIA-1 (yeast Nam8), both of which have been linked to human disease 5,6 . In the prespliceosome, the U1 snRNP associates with the U2 snRNP through a stable contact with the U2 3' domain and a transient yeast-specific contact with the U2 SF3b-containing 5' region, leaving its tri-snRNP-binding interface fully exposed. The results suggest mechanisms for 5' splice site transfer to the U6 ACAGAGA region within the assembled spliceosome and for its subsequent conversion to the activation-competent B-complex spliceosome 7,8 . Taken together, the data provide a working model to investigate the early steps of spliceosome assembly.


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge, UK. kn@mrc-lmb.cam.ac.uk.,MRC Laboratory of Molecular Biology, Cambridge, UK.,Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria. clemens.plaschka@imp.ac.at.,MRC Laboratory of Molecular Biology, Cambridge, UK. clemens.plaschka@imp.ac.at.,MRC Laboratory of Molecular Biology, Cambridge, UK. pclin@mrc-lmb.cam.ac.uk.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
U1 small nuclear ribonucleoprotein A,U1 small nuclear ribonucleoprotein A,U1 small nuclear ribonucleoprotein A,U1 small nuclear ribonucleoprotein A,U1 small nuclear ribonucleoprotein A
A
298Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MUD1
Find proteins for P32605 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32605
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
U1 small nuclear ribonucleoprotein 70 kDa homolog,U1 small nuclear ribonucleoprotein 70 kDa homolog,U1 small nuclear ribonucleoprotein 70 kDa homolog
B
300Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SNP1
Find proteins for Q00916 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q00916
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
U1 small nuclear ribonucleoprotein C
C
231Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: YHC1
Find proteins for Q05900 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q05900
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing factor 39
D
629Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRP39
Find proteins for P39682 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P39682
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
U1 small nuclear ribonucleoprotein component PRP42
E
544Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRP42 (MUD16, SNU65)
Find proteins for Q03776 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q03776
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Protein NAM8
F
523Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: NAM8 (MRE2)
Find proteins for Q00539 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q00539
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
56 kDa U1 small nuclear ribonucleoprotein component
G
492Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SNU56 (MUD10)
Find proteins for Q03782 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q03782
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Protein LUC7,Protein LUC7,Protein LUC7
H
261Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: LUC7 (EPE1, EXM2)
Find proteins for Q07508 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q07508
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
U1 small nuclear ribonucleoprotein component SNU71
J
620Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SNU71
Find proteins for P53207 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P53207
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
U2 snRNP component HSH155
O
971Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: HSH155
Find proteins for P49955 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P49955
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor RSE1
P
1361Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RSE1 (SAP130)
Find proteins for Q04693 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q04693
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Cold sensitive U2 snRNA suppressor 1
Q
435Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CUS1
Find proteins for Q02554 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q02554
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Protein HSH49
R
213Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: HSH49
Find proteins for Q99181 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q99181
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor RDS3
S
107Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RDS3
Find proteins for Q06835 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q06835
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor PRP9
T
530Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRP9
Find proteins for P19736 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P19736
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor PRP11,Pre-mRNA-splicing factor PRP11,Pre-mRNA-splicing factor PRP11
U
266Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRP11 (PRP10, RNA11)
Find proteins for Q07350 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q07350
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor PRP21
V
280Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRP21 (SPP91)
Find proteins for P32524 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32524
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
U2 small nuclear ribonucleoprotein A'
W
238Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: LEA1
Find proteins for Q08963 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q08963
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Unknown
X
51N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
U2 small nuclear ribonucleoprotein B''
Y
111Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MSL1
Find proteins for P40567 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MSL1
Go to UniProtKB:  P40567
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
RDS3 complex subunit 10
Z
85Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: YSF3 (RCP10)
Find proteins for P0C074 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0C074
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein-associated protein B
b, s
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: 26
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D3
d, v
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: 27
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein E
e, w
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: 28
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein F
f, x
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: 29
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein G
g, y
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: 30
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D1
h, t
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: 31
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D2
i, u
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
U1 snRNA,U1 snRNA,U1 snRNA,U1 snRNA,U1 snRNA1407Saccharomyces cerevisiae
Entity ID: 2
MoleculeChainsLengthOrganism
U2 snRNA2143Saccharomyces cerevisiae
Entity ID: 11
MoleculeChainsLengthOrganism
Yeast UBC4 pre-mRNA (mutant)I38Saccharomyces cerevisiae
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
C, H, S, T, U
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
1, 2
RNA LINKINGC9 H13 N2 O9 PU
UNK
Query on UNK
A, B, H, U, X
L-PEPTIDE LINKINGC4 H9 N O2

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N
Query on N
1
RNA LINKINGC5 H11 O7 P

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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 CouncilUnited Kingdom693087 - SPLICE3D

Revision History 

  • Version 1.0: 2018-08-22
    Type: Initial release