6G90

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 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
  • Primary Citation of Related Structures:  
    6G90

  • 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 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 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.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
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 A298Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P32605 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32605 
Go to UniProtKB:  P32605
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
U1 small nuclear ribonucleoprotein 70 kDa homolog,U1 small nuclear ribonucleoprotein 70 kDa homolog,U1 small nuclear ribonucleoprotein 70 kDa homolog B300Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q00916 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q00916 
Go to UniProtKB:  Q00916
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
U1 small nuclear ribonucleoprotein C C231Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q05900 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q05900 
Go to UniProtKB:  Q05900
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 39 D629Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P39682 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P39682 
Go to UniProtKB:  P39682
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
U1 small nuclear ribonucleoprotein component PRP42 E544Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q03776 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q03776 
Go to UniProtKB:  Q03776
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Protein NAM8 F523Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q00539 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q00539 
Go to UniProtKB:  Q00539
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
56 kDa U1 small nuclear ribonucleoprotein component G492Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q03782 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q03782 
Go to UniProtKB:  Q03782
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Protein LUC7,Protein LUC7,Protein LUC7 H261Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q07508 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q07508 
Go to UniProtKB:  Q07508
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
U1 small nuclear ribonucleoprotein component SNU71 J620Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P53207 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53207 
Go to UniProtKB:  P53207
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
U2 snRNP component HSH155 O971Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P49955 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P49955 
Go to UniProtKB:  P49955
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor RSE1 P1361Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q04693 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q04693 
Go to UniProtKB:  Q04693
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Cold sensitive U2 snRNA suppressor 1 Q435Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q02554 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q02554 
Go to UniProtKB:  Q02554
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Protein HSH49 R213Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q99181 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q99181 
Go to UniProtKB:  Q99181
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor RDS3 S107Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q06835 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q06835 
Go to UniProtKB:  Q06835
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor PRP9 T530Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P19736 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P19736 
Go to UniProtKB:  P19736
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor PRP11,Pre-mRNA-splicing factor PRP11,Pre-mRNA-splicing factor PRP11 U266Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q07350 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q07350 
Go to UniProtKB:  Q07350
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor PRP21 V280Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P32524 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32524 
Go to UniProtKB:  P32524
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein A' W238Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q08963 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q08963 
Go to UniProtKB:  Q08963
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown X51Saccharomyces cerevisiaeMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein B'' Y111Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P40567 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40567 
Go to UniProtKB:  P40567
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
RDS3 complex subunit 10 Z85Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0C074 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0C074 
Go to UniProtKB:  P0C074
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated protein B bs196Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P40018 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40018 
Go to UniProtKB:  P40018
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3 dv101Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P43321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P43321 
Go to UniProtKB:  P43321
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein E ew94Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q12330 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12330 
Go to UniProtKB:  Q12330
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein F fx86Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P54999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P54999 
Go to UniProtKB:  P54999
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein G gy77Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P40204 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40204 
Go to UniProtKB:  P40204
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1 ht146Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q02260 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q02260 
Go to UniProtKB:  Q02260
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2 iu110Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q06217 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q06217 
Go to UniProtKB:  Q06217
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
U1 snRNA,U1 snRNA,U1 snRNA,U1 snRNA,U1 snRNA1407Saccharomyces cerevisiae
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
U2 snRNA2143Saccharomyces cerevisiae
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 11
MoleculeChainsLengthOrganismImage
Yeast UBC4 pre-mRNA (mutant)I38Saccharomyces cerevisiae
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMC_U105184330
European Research CouncilUnited Kingdom693087 - SPLICE3D

Revision History  (Full details and data files)

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