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 1.3 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: https://doi.org/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). 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.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 82,413Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SNU114B [auth C]1,008Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC21C [auth J]135Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor PRP46D [auth O]451Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing protein 45E [auth P]379Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SLT11F [auth Q]364Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC2G [auth R]339Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC15H [auth S]175Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor BUD31I [auth T]157Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC22J [auth Z]577Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CEF1,Pre-mRNA-splicing factor CEF1,Cef1,Pre-mRNA-splicing factor CEF1Q [auth c]579Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CLF1,Pre-mRNA-splicing factor CLF1,Clf1R [auth d]652Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF2S [auth I]215Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
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 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 17U [auth n]455Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 19V [auth o],
W [auth p],
X [auth q],
Y [auth r]
503Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SNT309Z [auth t]175Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated protein BAA [auth k],
HA [auth F]
196Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EBA [auth i],
IA [auth G]
94Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FCA [auth h],
JA [auth H]
86Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GDA [auth j],
KA [auth K]
77Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3EA [auth l],
LA [auth U]
101Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1FA [auth m],
MA [auth V]
146Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2GA [auth g],
NA [auth W]
110Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein B''OA [auth X]111Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein A'PA [auth Y]238Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16RA [auth e]1,071Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.6.4.13
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 18SA [auth f]251Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains LengthOrganismImage
5'-exonK [auth B]13Saccharomyces cerevisiae S288C
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Entity ID: 12
MoleculeChains LengthOrganismImage
5'-intron-lariatL [auth N]15Saccharomyces cerevisiae S288C
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Entity ID: 13
MoleculeChains LengthOrganismImage
U5 snRNAM [auth D]214Saccharomyces cerevisiae S288C
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Entity ID: 14
MoleculeChains LengthOrganismImage
Saccharomyces cerevisiae S288c SNR6 snRNAN [auth E]112Saccharomyces cerevisiae S288C
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Entity ID: 15
MoleculeChains LengthOrganismImage
RNA (91-MER)O [auth L]1,175Saccharomyces cerevisiae S288C
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Entity ID: 16
MoleculeChains LengthOrganismImage
3'-intron-lariatP [auth M]23Saccharomyces cerevisiae S288C
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Entity ID: 33
MoleculeChains LengthOrganismImage
3'-exon-intronQA [auth b]14Saccharomyces cerevisiae S288C
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Small Molecules
Ligands 3 Unique
IDChains Name / 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
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
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
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION1.4

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
  • Version 1.3: 2024-03-20
    Changes: Data collection, Database references, Derived calculations