6N7R

Saccharomyces cerevisiae spliceosomal E complex (ACT1)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

A unified mechanism for intron and exon definition and back-splicing.

Li, X.Liu, S.Zhang, L.Issaian, A.Hill, R.C.Espinosa, S.Shi, S.Cui, Y.Kappel, K.Das, R.Hansen, K.C.Zhou, Z.H.Zhao, R.

(2019) Nature 573: 375-380

  • DOI: 10.1038/s41586-019-1523-6
  • Primary Citation of Related Structures:  
    6N7P, 6N7R

  • PubMed Abstract: 
  • The molecular mechanisms of exon definition and back-splicing are fundamental unanswered questions in pre-mRNA splicing. Here we report cryo-electron microscopy structures of the yeast spliceosomal E complex assembled on introns, providing a view of the earliest event in the splicing cycle that commits pre-mRNAs to splicing ...

    The molecular mechanisms of exon definition and back-splicing are fundamental unanswered questions in pre-mRNA splicing. Here we report cryo-electron microscopy structures of the yeast spliceosomal E complex assembled on introns, providing a view of the earliest event in the splicing cycle that commits pre-mRNAs to splicing. The E complex architecture suggests that the same spliceosome can assemble across an exon, and that it either remodels to span an intron for canonical linear splicing (typically on short exons) or catalyses back-splicing to generate circular RNA (on long exons). The model is supported by our experiments, which show that an E complex assembled on the middle exon of yeast EFM5 or HMRA1 can be chased into circular RNA when the exon is sufficiently long. This simple model unifies intron definition, exon definition, and back-splicing through the same spliceosome in all eukaryotes and should inspire experiments in many other systems to understand the mechanism and regulation of these processes.


    Organizational Affiliation

    RNA Bioscience Initiative, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA. rui.zhao@cuanschutz.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
U1 small nuclear ribonucleoprotein 70 kDa homolog A300Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNP1YIL061C
Find proteins for Q00916 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
U1 small nuclear ribonucleoprotein C B231Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: YHC1YLR298CL8003.21
Find proteins for Q05900 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
U1 small nuclear ribonucleoprotein A C350Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MUD1YBR119WYBR0915
Find proteins for P32605 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
U1 small nuclear ribonucleoprotein component PRP42 D544Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP42MUD16SNU65YDR235WYD8419.02
Find proteins for Q03776 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 39 E629Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP39YML046WYM9827.06
Find proteins for P39682 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Protein NAM8 F523Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NAM8MRE2YHR086W
Find proteins for Q00539 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
56 kDa U1 small nuclear ribonucleoprotein component G492Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNU56MUD10YDR240C
Find proteins for Q03782 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
U1 small nuclear ribonucleoprotein component SNU71,U1 small nuclear ribonucleoprotein component SNU71,Snu71 H89Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNU71
Find proteins for P53207 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Protein LUC7 I261Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LUC7EPE1EXM2YDL087C
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated protein B K196Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMB1YER029C
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1 L146Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMD1YGR074W
Find proteins for Q02260 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2 M110Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMD2YLR275WL9328.5
Find proteins for Q06217 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3 N101Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMD3YLR147CL9634.6
Find proteins for P43321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein E O94Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SME1YOR159C
Find proteins for Q12330 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein F P86Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMX3YPR182WP9705.4
Find proteins for P54999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein G Q77Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMX2SNP2YFL017W-AYFL017Bw
Find proteins for P40204 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 17
MoleculeChainsLengthOrganismImage
U1 snRNAR568Saccharomyces cerevisiae
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Entity ID: 18
MoleculeChainsLengthOrganismImage
ACT1 pre-mRNAr240Saccharomyces cerevisiae S288C
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesGM126157
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesGM114178
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesGM071940
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesAI094386

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-18
    Type: Initial release
  • Version 1.1: 2019-10-02
    Changes: Data collection, Database references
  • Version 2.0: 2019-12-18
    Changes: Author supporting evidence, Polymer sequence