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 executed by the step II catalytically activated spliceosome (known as the C* complex) ...

    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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 8A2413Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP8DBF3DNA39RNA8SLT21USA2YHR165C
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SNU114B [auth C]1008Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNU114GIN10YKL173WYKL637
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC21C [auth J]135Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CWC21YDR482C
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor PRP46D [auth O]451Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP46CWC1NTC50YPL151CP2594
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing protein 45E [auth P]379Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP45FUN20YAL032C
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SLT11F [auth Q]364Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ECM2SLT11YBR065CYBR0614
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC2G [auth R]339Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CWC2NTC40SLC3YDL209CD1041
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC15H [auth S]175Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CWC15YDR163WYD8358.17
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor BUD31I [auth T]157Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BUD31CWC14YCR063WYCR63WYCR903
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Entity ID: 10
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Pre-mRNA-splicing factor CWC22J [auth Z]577Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CWC22YGR278W
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CEF1,Pre-mRNA-splicing factor CEF1,Cef1,Pre-mRNA-splicing factor CEF1Q [auth c]579Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CEF1
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Entity ID: 18
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Pre-mRNA-splicing factor CLF1,Pre-mRNA-splicing factor CLF1,Clf1R [auth d]652Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CLF1
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Entity ID: 19
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Pre-mRNA-splicing factor SYF2S [auth I]215Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SYF2NTC31YGR129W
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Entity ID: 20
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Syf1,Pre-mRNA-splicing factor SYF1,Syf1,Pre-mRNA-splicing factor SYF1,Syf1,Pre-mRNA-splicing factor SYF1,Syf1T [auth v]858Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SYF1
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Entity ID: 21
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Pre-mRNA-processing factor 17U [auth n]455Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CDC40PRP17SLU4XRS2YDR364CD9481.11
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 19V [auth o],
W [auth p],
X [auth q],
Y [auth r]
503Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP19PSO4YLL036C
EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
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Entity ID: 23
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Pre-mRNA-splicing factor SNT309Z [auth t]175Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNT309NTC25YPR101W
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated protein BHA [auth F],
AA [auth k]
196Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMB1YER029C
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EIA [auth G],
BA [auth i]
94Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SME1YOR159C
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Entity ID: 26
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Small nuclear ribonucleoprotein FJA [auth H],
CA [auth h]
86Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMX3YPR182WP9705.4
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GKA [auth K],
DA [auth j]
77Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMX2SNP2YFL017W-AYFL017Bw
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3LA [auth U],
EA [auth l]
101Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMD3YLR147CL9634.6
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1MA [auth V],
FA [auth m]
146Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMD1YGR074W
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Entity ID: 30
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Small nuclear ribonucleoprotein Sm D2NA [auth W],
GA [auth g]
110Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMD2YLR275WL9328.5
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Entity ID: 31
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U2 small nuclear ribonucleoprotein B''OA [auth X]111Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MSL1YIR009WYIB9W
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Entity ID: 32
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U2 small nuclear ribonucleoprotein A'PA [auth Y]238Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LEA1YPL213W
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16RA [auth e]1071Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP16YKR086WYKR406
EC: 3.6.4.13
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 18SA [auth f]251Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP18YGR006W
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Entity ID: 11
MoleculeChainsLengthOrganismImage
5'-exonK [auth B]13Saccharomyces cerevisiae S288C
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Entity ID: 12
MoleculeChainsLengthOrganismImage
5'-intron-lariatL [auth N]15Saccharomyces cerevisiae S288C
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Entity ID: 13
MoleculeChainsLengthOrganismImage
U5 snRNAM [auth D]214Saccharomyces cerevisiae S288C
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Entity ID: 14
MoleculeChainsLengthOrganismImage
Saccharomyces cerevisiae S288c SNR6 snRNAN [auth E]112Saccharomyces cerevisiae S288C
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Entity ID: 15
MoleculeChainsLengthOrganismImage
RNA (91-MER)O [auth L]1175Saccharomyces cerevisiae S288C
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Entity ID: 16
MoleculeChainsLengthOrganismImage
3'-intron-lariatP [auth M]23Saccharomyces cerevisiae S288C
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Entity ID: 33
MoleculeChainsLengthOrganismImage
3'-exon-intronQA [auth b]14Saccharomyces cerevisiae S288C
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

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TA [auth C]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
ZN
Query on ZN

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AB [auth T],
VA [auth Q],
WA [auth Q],
XA [auth R],
YA [auth T],
AB [auth T],
VA [auth Q],
WA [auth Q],
XA [auth R],
YA [auth T],
ZA [auth T]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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BB [auth B],
CB [auth E],
DB [auth E],
EB [auth E],
FB [auth E],
BB [auth B],
CB [auth E],
DB [auth E],
EB [auth E],
FB [auth E],
UA [auth C]
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

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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