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: 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 ...

    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)  |  Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 8 A2413Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P33334 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P33334 
Go to UniProtKB:  P33334
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Protein CWC16 D278Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P28320 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P28320 
Go to UniProtKB:  P28320
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC25 F179Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P53854 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53854 
Go to UniProtKB:  P53854
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SNU114 C1008Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P36048 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P36048 
Go to UniProtKB:  P36048
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
ISY1 G235Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P21374 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P21374 
Go to UniProtKB:  P21374
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
CWC22 H591Saccharomyces cerevisiaeMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
PRP46 J451Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q12417 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12417 
Go to UniProtKB:  Q12417
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing protein 45 K379Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P28004 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P28004 
Go to UniProtKB:  P28004
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor BUD31 L157Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P25337 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P25337 
Go to UniProtKB:  P25337
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
CWC2 M339Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q12046 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12046 
Go to UniProtKB:  Q12046
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SLT11 N364Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P38241 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38241 
Go to UniProtKB:  P38241
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
CEF1 O590Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q03654 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q03654 
Go to UniProtKB:  Q03654
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
CWC15 P175Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q03772 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q03772 
Go to UniProtKB:  Q03772
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC21 R135Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q03375 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q03375 
Go to UniProtKB:  Q03375
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
CLF1 S687Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q12309 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12309 
Go to UniProtKB:  Q12309
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
SYF1 T859Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q04048 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q04048 
Go to UniProtKB:  Q04048
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated protein B bk196Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P40018 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40018 
Go to UniProtKB:  P40018
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3 dn101Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P43321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P43321 
Go to UniProtKB:  P43321
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein E ep94Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q12330 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12330 
Go to UniProtKB:  Q12330
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein F fq86Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P54999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P54999 
Go to UniProtKB:  P54999
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein G gr77Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P40204 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40204 
Go to UniProtKB:  P40204
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1 hl146Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q02260 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q02260 
Go to UniProtKB:  Q02260
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2 jm110Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q06217 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q06217 
Go to UniProtKB:  Q06217
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein A' W238Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q08963 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q08963 
Go to UniProtKB:  Q08963
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein B'' Y111Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P40567 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40567 
Go to UniProtKB:  P40567
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
unknown x132Saccharomyces cerevisiaeMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
U5 snRNA (small nuclear RNA)U179Saccharomyces cerevisiae
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    Exon 1 (5' exon) of UBC4 pre-mRNAE16Saccharomyces cerevisiae
    Find similar nucleic acids by: 
    (by identity cutoff)  |  Structure
    Entity ID: 3
    MoleculeChainsLengthOrganismImage
    Intron of UBC4 pre-mRNAI76Saccharomyces cerevisiae
    Find similar nucleic acids by: 
    (by identity cutoff)  |  Structure
    Entity ID: 4
    MoleculeChainsLengthOrganismImage
    U2 snRNA (small nuclear RNA)Z1175Saccharomyces cerevisiae
    Find similar nucleic acids by: 
    (by identity cutoff)  |  Structure
    Entity ID: 5
    MoleculeChainsLengthOrganismImage
    U6 snRNA (small nuclear RNA)V112Saccharomyces cerevisiae
    Experimental Data & Validation

    Experimental Data

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

    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