6N7R

Saccharomyces cerevisiae spliceosomal E complex (ACT1)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.2 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:  

  • 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 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

    Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,RNA Bioscience Initiative, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA. rui.zhao@cuanschutz.edu.,Department of Physics, Stanford University, Stanford, CA, USA.,Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA, USA. hong.zhou@ucla.edu.,Department of Biochemistry, Stanford University, Stanford, CA, USA.,Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA. rui.zhao@cuanschutz.edu.,Electron Imaging Center for Nanomachines, UCLA, Los Angeles, CA, USA.,Biophysics Program, Stanford University, Stanford, CA, USA.,Electron Imaging Center for Nanomachines, UCLA, Los Angeles, CA, USA. hong.zhou@ucla.edu.,Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
U1 small nuclear ribonucleoprotein 70 kDa homolog
A
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: 2
MoleculeChainsSequence LengthOrganismDetails
U1 small nuclear ribonucleoprotein C
B
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: 3
MoleculeChainsSequence LengthOrganismDetails
U1 small nuclear ribonucleoprotein A
C
350Saccharomyces 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 component PRP42
D
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: 5
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing factor 39
E
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: 6
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: 7
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: 8
MoleculeChainsSequence LengthOrganismDetails
U1 small nuclear ribonucleoprotein component SNU71,U1 small nuclear ribonucleoprotein component SNU71,Snu71
H
89Saccharomyces 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: 9
MoleculeChainsSequence LengthOrganismDetails
Protein LUC7
I
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: 10
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein-associated protein B
K
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: 11
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D1
L
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: 12
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D2
M
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: 13
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D3
N
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: 14
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein E
O
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: 15
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein F
P
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: 16
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein G
Q
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: 17
MoleculeChainsLengthOrganism
U1 snRNAR568Saccharomyces cerevisiae
Entity ID: 18
MoleculeChainsLengthOrganism
ACT1 pre-mRNAr240Saccharomyces cerevisiae S288C
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
H
L-PEPTIDE LINKINGC4 H9 N O2

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N
Query on N
r
RNA LINKINGC5 H11 O7 P

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.2 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
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 

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