5WSG

Cryo-EM structure of the Catalytic Step II spliceosome (C* complex) at 4.0 angstrom resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of a yeast step II catalytically activated spliceosome

Yan, C.Wan, R.Bai, R.Huang, G.Shi, Y.

(2017) Science 355: 149-155

  • DOI: 10.1126/science.aak9979
  • Primary Citation of Related Structures:  
    5WSG

  • PubMed Abstract: 
  • Each cycle of precursor messenger RNA (pre-mRNA) splicing comprises two sequential reactions, first freeing the 5' exon and generating an intron lariat-3' exon and then ligating the two exons and releasing the intron lariat. The second reaction is ex ...

    Each cycle of precursor messenger RNA (pre-mRNA) splicing comprises two sequential reactions, first freeing the 5' exon and generating an intron lariat-3' exon and then ligating the two exons and releasing the intron lariat. The second reaction is executed by the step II catalytically activated spliceosome (known as the C* complex). Here, we present the cryo-electron microscopy structure of a C* complex from Saccharomyces cerevisiae at an average resolution of 4.0 angstroms. Compared with the preceding spliceosomal complex (C complex), the lariat junction has been translocated by 15 to 20 angstroms to vacate space for the incoming 3'-exon sequences. The step I splicing factors Cwc25 and Yju2 have been dissociated from the active site. Two catalytic motifs from Prp8 (the 1585 loop and the β finger of the ribonuclease H-like domain), along with the step II splicing factors Prp17 and Prp18 and other surrounding proteins, are poised to assist the second transesterification. These structural features, together with those reported for other spliceosomal complexes, yield a near-complete mechanistic picture on the splicing cycle.


    Organizational Affiliation

    Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China. shi-lab@tsinghua.edu.cn.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 8A2413Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP8DBF3DNA39RNA8SLT21USA2YHR165C
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: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SNU114C1008Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNU114GIN10YKL173WYKL637
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: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC21J135Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CWC21YDR482C
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: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor PRP46O451Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP46CWC1NTC50YPL151CP2594
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: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing protein 45P379Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP45FUN20YAL032C
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: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SLT11Q364Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ECM2SLT11YBR065CYBR0614
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: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC2R339Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CWC2NTC40SLC3YDL209CD1041
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: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC15S175Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CWC15YDR163WYD8358.17
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: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor BUD31T157Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BUD31CWC14YCR063WYCR63WYCR903
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: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC22Z577Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CWC22YGR278W
Find proteins for P53333 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53333 
Go to UniProtKB:  P53333
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CEF1,Pre-mRNA-splicing factor CEF1,Cef1,Pre-mRNA-splicing factor CEF1c579Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CEF1
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
Pre-mRNA-splicing factor CLF1,Pre-mRNA-splicing factor CLF1,Clf1d652Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CLF1
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: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF2I215Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SYF2NTC31YGR129W
Find proteins for P53277 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53277 
Go to UniProtKB:  P53277
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Syf1,Pre-mRNA-splicing factor SYF1,Syf1,Pre-mRNA-splicing factor SYF1,Syf1,Pre-mRNA-splicing factor SYF1,Syf1v858Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SYF1
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: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 17n455Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CDC40PRP17SLU4XRS2YDR364CD9481.11
Find proteins for P40968 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40968 
Go to UniProtKB:  P40968
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 19opqr503Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP19PSO4YLL036C
EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
Find proteins for P32523 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32523 
Go to UniProtKB:  P32523
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SNT309t175Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNT309NTC25YPR101W
Find proteins for Q06091 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q06091 
Go to UniProtKB:  Q06091
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated protein BFk196Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMB1YER029C
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: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EGi94Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SME1YOR159C
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: 26
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FHh86Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMX3YPR182WP9705.4
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: 27
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GKj77Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMX2SNP2YFL017W-AYFL017Bw
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: 28
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3Ul101Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMD3YLR147CL9634.6
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: 29
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1Vm146Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMD1YGR074W
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: 30
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2Wg110Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMD2YLR275WL9328.5
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: 31
MoleculeChainsSequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein B''X111Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MSL1YIR009WYIB9W
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: 32
MoleculeChainsSequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein A'Y238Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LEA1YPL213W
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: 34
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16e1071Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP16YKR086WYKR406
EC: 3.6.4.13
Find proteins for P15938 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P15938 
Go to UniProtKB:  P15938
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 18f251Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP18YGR006W
Find proteins for P33411 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P33411 
Go to UniProtKB:  P33411
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 11
    MoleculeChainsLengthOrganismImage
    5'-exonB13Saccharomyces cerevisiae S288C
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 12
      MoleculeChainsLengthOrganismImage
      5'-intron-lariatN15Saccharomyces cerevisiae S288C
      Find similar nucleic acids by: 
      (by identity cutoff)  |  Structure
      Entity ID: 13
      MoleculeChainsLengthOrganismImage
      U5 snRNAD214Saccharomyces cerevisiae S288C
      Find similar nucleic acids by: 
      (by identity cutoff)  |  Structure
      Entity ID: 14
      MoleculeChainsLengthOrganismImage
      Saccharomyces cerevisiae S288c SNR6 snRNAE112Saccharomyces cerevisiae S288C
      Find similar nucleic acids by: 
      (by identity cutoff)  |  Structure
      Entity ID: 15
      MoleculeChainsLengthOrganismImage
      RNA (91-MER)L1175Saccharomyces cerevisiae S288C
      Find similar nucleic acids by: 
      (by identity cutoff)  |  Structure
      Entity ID: 16
      MoleculeChainsLengthOrganismImage
      3'-intron-lariatM23Saccharomyces cerevisiae S288C
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 33
        MoleculeChainsLengthOrganismImage
        3'-exon-intronb14Saccharomyces cerevisiae S288C
        Small Molecules
        Ligands 3 Unique
        IDChainsName / Formula / InChI Key2D Diagram3D Interactions
        GTP
        Query on GTP

        Download CCD File 
        C
        GUANOSINE-5'-TRIPHOSPHATE
        C10 H16 N5 O14 P3
        XKMLYUALXHKNFT-UUOKFMHZSA-N
         Ligand Interaction
        ZN
        Query on ZN

        Download CCD File 
        Q, R, T
        ZINC ION
        Zn
        PTFCDOFLOPIGGS-UHFFFAOYSA-N
         Ligand Interaction
        MG
        Query on MG

        Download CCD File 
        B, C, E
        MAGNESIUM ION
        Mg
        JLVVSXFLKOJNIY-UHFFFAOYSA-N
         Ligand Interaction
        Experimental Data & Validation

        Experimental Data

        • Method: ELECTRON MICROSCOPY
        • Resolution: 4.00 Å
        • Aggregation State: PARTICLE 
        • Reconstruction Method: SINGLE PARTICLE 

        Structure Validation

        View Full Validation Report



        Entry History 

        Deposition Data

        Revision History 

        • Version 1.0: 2017-01-25
          Type: Initial release
        • Version 1.1: 2017-08-09
          Changes: Data collection, Structure summary
        • Version 1.2: 2019-10-09
          Changes: Data collection, Other