5GMK

Cryo-EM structure of the Catalytic Step I spliceosome (C complex) at 3.4 angstrom resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 2.0 of the entry. See complete history


Literature

Structure of a yeast catalytic step I spliceosome at 3.4 angstrom resolution

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

(2016) Science 353: 895-904

  • DOI: https://doi.org/10.1126/science.aag2235
  • Primary Citation of Related Structures:  
    5GMK

  • PubMed Abstract: 

    Each cycle of pre-messenger RNA splicing, carried out by the spliceosome, comprises two sequential transesterification reactions, which result in the removal of an intron and the joining of two exons. Here we report an atomic structure of a catalytic step I spliceosome (known as the C complex) from Saccharomyces cerevisiae, as determined by cryo-electron microscopy at an average resolution of 3.4 angstroms. In the structure, the 2'-OH of the invariant adenine nucleotide in the branch point sequence (BPS) is covalently joined to the phosphate at the 5' end of the 5' splice site (5'SS), forming an intron lariat. The freed 5' exon remains anchored to loop I of U5 small nuclear RNA (snRNA), and the 5'SS and BPS of the intron form duplexes with conserved U6 and U2 snRNA sequences, respectively. Specific placement of these RNA elements at the catalytic cavity of Prp8 is stabilized by 15 protein components, including Snu114 and the splicing factors Cwc21, Cwc22, Cwc25, and Yju2. These features, representing the conformation of the spliceosome after the first-step reaction, predict structural changes that are needed for the execution of the second-step transesterification reaction.


  • 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: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC21I [auth J]135Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor PRP46J [auth O]451Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing protein 45K [auth P]379Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SLT11L [auth Q]364Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC2M [auth R]339Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC15N [auth S]175Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor BUD31O [auth T]157Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC22P [auth Z]577Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CEF1Q [auth c]587Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CLF1R [auth d]687Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Protein CWC16S [auth F]278Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC25T [auth G]179Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor ISY1U [auth H]235Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF2V [auth I]215Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF1W [auth v]859Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 17X [auth n]455Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 19AA [auth q],
BA [auth r],
Y [auth o],
Z [auth p]
503Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 6.3.2
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SNT309CA [auth t]175Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated protein BDA [auth k],
KA [auth s]
196Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EEA [auth i],
LA [auth u]
94Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FFA [auth h],
MA [auth w]
86Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GGA [auth j],
NA [auth x]
77Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3HA [auth l],
OA [auth y]
101Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1IA [auth m],
PA [auth z]
146Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2JA [auth g],
QA [auth e]
110Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein B''RA [auth a]111Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein A'SA [auth b]238Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 3
MoleculeChains LengthOrganismImage
U5 snRNAC [auth D]214Saccharomyces cerevisiae S288C
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Entity ID: 4
MoleculeChains LengthOrganismImage
U6 snRNAD [auth E]112Saccharomyces cerevisiae S288C
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Entity ID: 5
MoleculeChains LengthOrganismImage
U2 snRNAE [auth L]1,175Saccharomyces cerevisiae S288C
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Entity ID: 6
MoleculeChains LengthOrganismImage
Intron_BPSF [auth M]29Saccharomyces cerevisiae S288C
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Entity ID: 7
MoleculeChains LengthOrganismImage
5'-ExonG [auth B]13Saccharomyces cerevisiae S288C
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Entity ID: 8
MoleculeChains LengthOrganismImage
5'-Splicing SiteH [auth N]15Saccharomyces 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 Q]
BB [auth Q]
CB [auth R]
DB [auth T]
EB [auth T]
AB [auth Q],
BB [auth Q],
CB [auth R],
DB [auth T],
EB [auth T],
FB [auth T],
GB [auth F]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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UA [auth C]
VA [auth E]
WA [auth E]
XA [auth E]
YA [auth E]
UA [auth C],
VA [auth E],
WA [auth E],
XA [auth E],
YA [auth E],
ZA [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 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: 2016-08-17
    Type: Initial release
  • Version 1.1: 2016-09-07
    Changes: Database references, Other
  • Version 1.2: 2016-09-14
    Changes: Other
  • Version 1.3: 2016-11-02
    Changes: Other
  • Version 1.4: 2016-12-21
    Changes: Structure summary
  • Version 1.5: 2019-11-06
    Changes: Data collection, Other
  • Version 2.0: 2024-03-27
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary