5GMK

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.4 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: 10.1126/science.aag2235

  • 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 ...

    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

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor 8
A
2413Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRP8 (DBF3, DNA39, RNA8, SLT21, USA2)
Find proteins for P33334 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P33334
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor SNU114
C
1008Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SNU114 (GIN10)
Find proteins for P36048 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P36048
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor CWC21
J
135Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CWC21
Find proteins for Q03375 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q03375
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor PRP46
O
451Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRP46 (CWC1, NTC50)
Find proteins for Q12417 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12417
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing protein 45
P
379Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRP45 (FUN20)
Find proteins for P28004 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P28004
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor SLT11
Q
364Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: ECM2 (SLT11)
Find proteins for P38241 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: ECM2
Go to UniProtKB:  P38241
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor CWC2
R
339Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CWC2 (NTC40, SLC3)
Find proteins for Q12046 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12046
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor CWC15
S
175Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CWC15
Find proteins for Q03772 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: CWC15
Go to UniProtKB:  Q03772
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor BUD31
T
157Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: BUD31 (CWC14)
Find proteins for P25337 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: BUD31
Go to UniProtKB:  P25337
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor CWC22
Z
577Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CWC22
Find proteins for P53333 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: CWC22
Go to UniProtKB:  P53333
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor CEF1
c
587Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CEF1 (NTC85)
Find proteins for Q03654 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q03654
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor CLF1
d
687Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CLF1 (NTC77, SYF3)
Find proteins for Q12309 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12309
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Protein CWC16
F
278Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: YJU2 (CWC16)
Find proteins for P28320 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P28320
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor CWC25
G
179Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CWC25
Find proteins for P53854 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: CWC25
Go to UniProtKB:  P53854
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor ISY1
H
235Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: ISY1 (NTC30, UTR3)
Find proteins for P21374 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: ISY1
Go to UniProtKB:  P21374
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor SYF2
I
215Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SYF2 (NTC31)
Find proteins for P53277 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: SYF2
Go to UniProtKB:  P53277
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor SYF1
v
859Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SYF1 (NTC90)
Find proteins for Q04048 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q04048
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing factor 17
n
455Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CDC40 (PRP17, SLU4, XRS2)
Find proteins for P40968 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: CDC40
Go to UniProtKB:  P40968
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing factor 19
o, p, q, r
503Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRP19 (PSO4)
EC: 2.3.2.27
Find proteins for P32523 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32523
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor SNT309
t
175Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SNT309 (NTC25)
Find proteins for Q06091 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q06091
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein-associated protein B
k, s
196Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SMB1
Find proteins for P40018 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40018
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein E
i, u
94Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SME1
Find proteins for Q12330 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12330
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein F
h, w
86Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SMX3
Find proteins for P54999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P54999
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein G
j, x
77Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SMX2 (SNP2)
Find proteins for P40204 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40204
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D3
l, y
101Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SMD3
Find proteins for P43321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P43321
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D1
m, z
146Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SMD1
Find proteins for Q02260 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q02260
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D2
g, e
110Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SMD2
Find proteins for Q06217 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q06217
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
U2 small nuclear ribonucleoprotein B''
a
111Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MSL1
Find proteins for P40567 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MSL1
Go to UniProtKB:  P40567
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
U2 small nuclear ribonucleoprotein A'
b
238Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: LEA1
Find proteins for Q08963 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q08963
Entity ID: 3
MoleculeChainsLengthOrganism
U5 snRNAD214Saccharomyces cerevisiae S288C
Entity ID: 4
MoleculeChainsLengthOrganism
U6 snRNAE112Saccharomyces cerevisiae S288C
Entity ID: 5
MoleculeChainsLengthOrganism
U2 snRNAL1175Saccharomyces cerevisiae S288C
Entity ID: 6
MoleculeChainsLengthOrganism
Intron_BPSM29Saccharomyces cerevisiae S288C
Entity ID: 7
MoleculeChainsLengthOrganism
5'-ExonB13Saccharomyces cerevisiae S288C
Entity ID: 8
MoleculeChainsLengthOrganism
5'-Splicing SiteN15Saccharomyces cerevisiae S288C
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

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

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Download CCD File 
C, E
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
c, d, v
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-08-17
    Type: Initial release
  • Version 1.1: 2016-09-07
    Type: Database references, Other
  • Version 1.2: 2016-09-14
    Type: Other
  • Version 1.3: 2016-11-02
    Type: Other
  • Version 1.4: 2016-12-21
    Type: Structure summary