6N7P

S. cerevisiae spliceosomal E complex (UBC4)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/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 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.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
U1 small nuclear ribonucleoprotein 70 kDa homolog300Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q00916 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q00916 
Go to UniProtKB:  Q00916
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00916
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
U1 small nuclear ribonucleoprotein C231Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q05900 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q05900 
Go to UniProtKB:  Q05900
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ05900
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
U1 small nuclear ribonucleoprotein A350Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P32605 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32605 
Go to UniProtKB:  P32605
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32605
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
U1 small nuclear ribonucleoprotein component PRP42544Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q03776 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q03776 
Go to UniProtKB:  Q03776
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03776
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 39629Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P39682 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P39682 
Go to UniProtKB:  P39682
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39682
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Protein NAM8523Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q00539 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q00539 
Go to UniProtKB:  Q00539
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00539
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
56 kDa U1 small nuclear ribonucleoprotein component492Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q03782 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q03782 
Go to UniProtKB:  Q03782
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03782
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
U1 small nuclear ribonucleoprotein component SNU71,U1 small nuclear ribonucleoprotein component SNU71,Snu71105Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P53207 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53207 
Go to UniProtKB:  P53207
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53207
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Protein LUC7261Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q07508 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q07508 
Go to UniProtKB:  Q07508
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07508
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing protein PRP40583Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P33203 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P33203 
Go to UniProtKB:  P33203
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP33203
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated protein B196Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P40018 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40018 
Go to UniProtKB:  P40018
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40018
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1146Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q02260 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q02260 
Go to UniProtKB:  Q02260
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02260
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2110Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q06217 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q06217 
Go to UniProtKB:  Q06217
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06217
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3101Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P43321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P43321 
Go to UniProtKB:  P43321
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43321
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein E94Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q12330 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12330 
Go to UniProtKB:  Q12330
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12330
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein F86Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P54999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P54999 
Go to UniProtKB:  P54999
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54999
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein G77Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P40204 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40204 
Go to UniProtKB:  P40204
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40204
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear cap-binding protein complex subunit 1T [auth X]861Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P34160 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P34160 
Go to UniProtKB:  P34160
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP34160
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear cap-binding protein subunit 2U [auth Y]208Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q08920 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q08920 
Go to UniProtKB:  Q08920
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08920
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 18
MoleculeChains LengthOrganismImage
U1 snRNA568Saccharomyces cerevisiae S288C
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 19
MoleculeChains LengthOrganismImage
UBC4 pre-mRNAS [auth r]253Saccharomyces cerevisiae S288C
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.1

Structure Validation

View Full Validation Report



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 1.2: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.3: 2024-03-20
    Changes: Data collection, Database references