5YLZ

Cryo-EM Structure of the Post-catalytic Spliceosome from Saccharomyces cerevisiae at 3.6 angstrom


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.6 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structure of the Post-catalytic Spliceosome from Saccharomyces cerevisiae

Bai, R.Yan, C.Wan, R.Lei, J.Shi, Y.

(2017) Cell 171: 1589-1598.e8

  • DOI: 10.1016/j.cell.2017.10.038

  • PubMed Abstract: 
  • Removal of an intron from a pre-mRNA by the spliceosome results in the ligation of two exons in the post-catalytic spliceosome (known as the P complex). Here, we present a cryo-EM structure of the P complex from Saccharomyces cerevisiae at an average ...

    Removal of an intron from a pre-mRNA by the spliceosome results in the ligation of two exons in the post-catalytic spliceosome (known as the P complex). Here, we present a cryo-EM structure of the P complex from Saccharomyces cerevisiae at an average resolution of 3.6 Å. The ligated exon is held in the active site through RNA-RNA contacts. Three bases at the 3' end of the 5' exon remain anchored to loop I of U5 small nuclear RNA, and the conserved AG nucleotides of the 3'-splice site (3'SS) are specifically recognized by the invariant adenine of the branch point sequence, the guanine base at the 5' end of the 5'SS, and an adenine base of U6 snRNA. The 3'SS is stabilized through an interaction with the 1585-loop of Prp8. The P complex structure provides a view on splice junction formation critical for understanding the complete splicing cycle.


    Organizational Affiliation

    Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, 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: 3
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: 7
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor SNT309
G
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: 8
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor SYF1
H
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: 9
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor CLF1
I
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: 10
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor CEF1
J
590Saccharomyces 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: 11
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor SYF2
K
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: 12
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor BUD31
L
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: 13
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing factor 17
T
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: 14
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor SLT11
M
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: 15
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor CWC2
N
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: 16
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: 17
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor CWC15
P
175Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CWC15
Find proteins for Q03772 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  Q03772
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing protein 45
Q
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: 19
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor CWC21
R
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: 20
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor CWC22
S
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: 21
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor 18
U
251Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRP18
Find proteins for P33411 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P33411
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor SLU7
V
382Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SLU7 (SLT17)
Find proteins for Q02775 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: SLU7
Go to UniProtKB:  Q02775
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP22
W
1145Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRP22
EC: 3.6.4.13
Find proteins for P24384 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P24384
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein-associated protein B
a, h
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: 25
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein E
b, i
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: 26
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein F
c, j
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: 27
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein G
d, k
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: 28
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D3
e, l
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: 29
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D1
f, m
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: 30
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D2
g, n
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: 31
MoleculeChainsSequence LengthOrganismDetails
U2 small nuclear ribonucleoprotein A'
o
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: 32
MoleculeChainsSequence LengthOrganismDetails
U2 small nuclear ribonucleoprotein B''
p
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: 33
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing factor 19
q, r, s, t
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: 2
MoleculeChainsLengthOrganism
U5 snRNAB214Saccharomyces cerevisiae S288C
Entity ID: 4
MoleculeChainsLengthOrganism
U6 snRNAD112Saccharomyces cerevisiae S288C
Entity ID: 5
MoleculeChainsLengthOrganism
mRNA/intron lariatE369Saccharomyces cerevisiae S288C
Entity ID: 6
MoleculeChainsLengthOrganism
U2 snRNAF1175Saccharomyces cerevisiae S288C
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
I6P
Query on I6P

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Download CCD File 
A
INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE
MYO-INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
 Ligand Interaction
ZN
Query on ZN

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Download CCD File 
L, M, N
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, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
N
Query on N
E
RNA LINKINGC5 H11 O7 P

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.6 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31621092
National Natural Science Foundation of ChinaChina31430020
Ministry of Science and Technology (China)China2016YFA0501100

Revision History 

  • Version 1.0: 2018-07-18
    Type: Initial release