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

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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 AC [auth A]298Saccharomyces cerevisiaeMutation(s): 0 
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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 homologD [auth B]300Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
U1 small nuclear ribonucleoprotein CE [auth C]231Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 39F [auth D]629Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
U1 small nuclear ribonucleoprotein component PRP42G [auth E]544Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 8
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Protein NAM8H [auth F]523Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
56 kDa U1 small nuclear ribonucleoprotein componentI [auth G]492Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 10
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Protein LUC7,Protein LUC7,Protein LUC7J [auth H]261Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
U1 small nuclear ribonucleoprotein component SNU71L [auth J]620Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
U2 snRNP component HSH155M [auth O]971Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor RSE1N [auth P]1361Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 15
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Cold sensitive U2 snRNA suppressor 1O [auth Q]435Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 16
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Protein HSH49P [auth R]213Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 17
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Pre-mRNA-splicing factor RDS3Q [auth S]107Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 18
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Pre-mRNA-splicing factor PRP9R [auth T]530Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor PRP11,Pre-mRNA-splicing factor PRP11,Pre-mRNA-splicing factor PRP11S [auth U]266Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 20
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Pre-mRNA-splicing factor PRP21T [auth V]280Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 21
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U2 small nuclear ribonucleoprotein A'U [auth W]238Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 22
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UnknownV [auth X]51Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein B''W [auth Y]111Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 24
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RDS3 complex subunit 10X [auth Z]85Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated protein BY [auth b], FA [auth s]196Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3Z [auth d], IA [auth v]101Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EAA [auth e], JA [auth w]94Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 28
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Small nuclear ribonucleoprotein FBA [auth f], KA [auth x]86Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GCA [auth g], LA [auth y]77Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1DA [auth h], GA [auth t]146Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2EA [auth i], HA [auth u]110Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
U1 snRNA,U1 snRNA,U1 snRNA,U1 snRNA,U1 snRNAA [auth 1]407Saccharomyces cerevisiae
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Entity ID: 2
MoleculeChainsLengthOrganismImage
U2 snRNAB [auth 2]143Saccharomyces cerevisiae
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Entity ID: 11
MoleculeChainsLengthOrganismImage
Yeast UBC4 pre-mRNA (mutant)K [auth I]38Saccharomyces cerevisiae
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
MA [auth C] , NA [auth H] , OA [auth H] , PA [auth S] , QA [auth S] , RA [auth S] , SA [auth T] , TA [auth T] , 
MA [auth C],  NA [auth H],  OA [auth H],  PA [auth S],  QA [auth S],  RA [auth S],  SA [auth T],  TA [auth T],  UA [auth U]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

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

Structure Validation

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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