5LJ3

Structure of the core of the yeast spliceosome immediately after branching


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Cryo-EM structure of the spliceosome immediately after branching.

Galej, W.P.Wilkinson, M.E.Fica, S.M.Oubridge, C.Newman, A.J.Nagai, K.

(2016) Nature 537: 197-201

  • DOI: https://doi.org/10.1038/nature19316
  • Primary Citation of Related Structures:  
    5LJ3, 5LJ5

  • PubMed Abstract: 

    Precursor mRNA (pre-mRNA) splicing proceeds by two consecutive transesterification reactions via a lariat-intron intermediate. Here we present the 3.8 Å cryo-electron microscopy structure of the spliceosome immediately after lariat formation. The 5'-splice site is cleaved but remains close to the catalytic Mg 2+ site in the U2/U6 small nuclear RNA (snRNA) triplex, and the 5'-phosphate of the intron nucleotide G(+1) is linked to the branch adenosine 2'OH. The 5'-exon is held between the Prp8 amino-terminal and linker domains, and base-pairs with U5 snRNA loop 1. Non-Watson-Crick interactions between the branch helix and 5'-splice site dock the branch adenosine into the active site, while intron nucleotides +3 to +6 base-pair with the U6 snRNA ACAGAGA sequence. Isy1 and the step-one factors Yju2 and Cwc25 stabilize docking of the branch helix. The intron downstream of the branch site emerges between the Prp8 reverse transcriptase and linker domains and extends towards the Prp16 helicase, suggesting a plausible mechanism of remodelling before exon ligation.


  • Organizational Affiliation

    MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 8F [auth A]2,413Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P33334 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P33334 
Go to UniProtKB:  P33334
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP33334
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Protein CWC16G [auth D]278Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P28320 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P28320 
Go to UniProtKB:  P28320
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28320
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC25H [auth F]179Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P53854 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53854 
Go to UniProtKB:  P53854
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53854
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SNU114I [auth C]1,008Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P36048 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P36048 
Go to UniProtKB:  P36048
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36048
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
ISY1J [auth G]235Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P21374 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P21374 
Go to UniProtKB:  P21374
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21374
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
CWC22K [auth H]591Saccharomyces cerevisiaeMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
PRP46L [auth J]451Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q12417 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12417 
Go to UniProtKB:  Q12417
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12417
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing protein 45M [auth K]379Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P28004 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P28004 
Go to UniProtKB:  P28004
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28004
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor BUD31N [auth L]157Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P25337 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P25337 
Go to UniProtKB:  P25337
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25337
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
CWC2O [auth M]339Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q12046 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12046 
Go to UniProtKB:  Q12046
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12046
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SLT11P [auth N]364Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P38241 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38241 
Go to UniProtKB:  P38241
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38241
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
CEF1Q [auth O]590Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q03654 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q03654 
Go to UniProtKB:  Q03654
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03654
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
CWC15R [auth P]175Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q03772 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q03772 
Go to UniProtKB:  Q03772
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03772
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC21S [auth R]135Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q03375 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q03375 
Go to UniProtKB:  Q03375
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03375
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
CLF1T [auth S]687Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q12309 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12309 
Go to UniProtKB:  Q12309
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12309
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
SYF1U [auth T]859Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q04048 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q04048 
Go to UniProtKB:  Q04048
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ04048
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated protein BEA [auth k],
V [auth b]
196Saccharomyces cerevisiaeMutation(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: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3HA [auth n],
W [auth d]
101Saccharomyces cerevisiaeMutation(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: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EIA [auth p],
X [auth e]
94Saccharomyces cerevisiaeMutation(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: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FJA [auth q],
Y [auth f]
86Saccharomyces cerevisiaeMutation(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: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GKA [auth r],
Z [auth g]
77Saccharomyces cerevisiaeMutation(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: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1AA [auth h],
FA [auth l]
146Saccharomyces cerevisiaeMutation(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: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2BA [auth j],
GA [auth m]
110Saccharomyces cerevisiaeMutation(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: 29
MoleculeChains Sequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein A'CA [auth W]238Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q08963 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q08963 
Go to UniProtKB:  Q08963
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08963
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein B''DA [auth Y]111Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P40567 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40567 
Go to UniProtKB:  P40567
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40567
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
unknownLA [auth x]132Saccharomyces cerevisiaeMutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
U5 snRNA (small nuclear RNA)A [auth U]179Saccharomyces cerevisiae
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
Exon 1 (5' exon) of UBC4 pre-mRNAB [auth E]16Saccharomyces cerevisiae
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains LengthOrganismImage
Intron of UBC4 pre-mRNAC [auth I]76Saccharomyces cerevisiae
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains LengthOrganismImage
U2 snRNA (small nuclear RNA)D [auth Z]1,175Saccharomyces cerevisiae
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains LengthOrganismImage
U6 snRNA (small nuclear RNA)E [auth V]112Saccharomyces cerevisiae
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download Ideal Coordinates CCD File 
PA [auth C]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
OA [auth D]
QA [auth L]
RA [auth L]
SA [auth L]
TA [auth M]
OA [auth D],
QA [auth L],
RA [auth L],
SA [auth L],
TA [auth M],
UA [auth N],
VA [auth N]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
MA [auth E],
NA [auth V]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTREFMAC5.8
RECONSTRUCTIONRELION1.4

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-03
    Type: Initial release
  • Version 1.1: 2016-09-21
    Changes: Database references
  • Version 1.2: 2017-08-30
    Changes: Data collection, Derived calculations
  • Version 1.3: 2018-10-03
    Changes: Data collection, Refinement description
  • Version 1.4: 2018-10-24
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.5: 2019-10-23
    Changes: Data collection, Other