EMD-7109

Single-particle
3.3 Å
EMD-7109
3D View Gallery
Deposition: 07/11/2017
Map released: 21/02/2018
Last modified: 14/10/2020
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Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-7109
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EMICSS annotations (xml)

S. cerevisiae spliceosomal post-catalytic P complex

EMD-7109

Single-particle
3.3 Å
EMD-7109
3D View Gallery
Deposition: 07/11/2017
Map released: 21/02/2018
Last modified: 14/10/2020
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Name: Spliceosomal P complex
Complex [1]
Name: Spliceosomal P complex
Natural source [1]
Organism: Saccharomyces cerevisiae
Complex Portal [2]
ID Name Overlap
CPX-1651 PRP19-associated complex 0.53
CPX-1651 PRP19-associated complex 0.51
RNA [5]
Name: U2 snRNA
Number of copies: 1
Natural source
Organism: Saccharomyces cerevisiae
Molecular weight
Experimental Theoretical Method
- 376 kDa -
Name: U5 snRNA
Number of copies: 1
Natural source
Organism: Saccharomyces cerevisiae
Molecular weight
Experimental Theoretical Method
- 68 kDa -
Name: U6 snRNA
Number of copies: 1
Natural source
Organism: Saccharomyces cerevisiae
Molecular weight
Experimental Theoretical Method
- 35 kDa -
Name: RNA (34-MER)
Number of copies: 1
Natural source
Organism: Saccharomyces cerevisiae
Molecular weight
Experimental Theoretical Method
- 10 kDa -
Name: RNA (59-MER)
Number of copies: 1
Natural source
Organism: Saccharomyces cerevisiae
Molecular weight
Experimental Theoretical Method
- 18 kDa -
Protein [31]
LEVO
Name: Pre-mRNA-splicing factor Prp8
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [20]
Biological process:
spliceosomal snRNP assembly mRNA splicing, via spliceosome mRNA 3'-splice site recognition mRNA 5'-splice site recognition generation of catalytic spliceosome for second transesterification step spliceosomal tri-snRNP complex assembly
Molecular function:
metallopeptidase activity U5 snRNA binding U2 snRNA binding pre-mRNA intronic binding U6 snRNA binding mRNA binding U1 snRNA binding isopeptidase activity
Cellular location:
spliceosomal complex cytoplasm U4/U6 x U5 tri-snRNP complex catalytic step 2 spliceosome nucleus U5 snRNP
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 279 kDa -
LEVO
Name: Pre-mRNA-splicing factor SNU114
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [17]
Biological process:
spliceosomal snRNP assembly spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) spliceosomal tri-snRNP complex assembly generation of catalytic spliceosome for first transesterification step mRNA splicing, via spliceosome
Molecular function:
translation elongation factor activity GTPase activity U5 snRNA binding GTP binding
Cellular location:
cytosol spliceosomal complex cytoplasm U5 snRNP U4/U6 x U5 tri-snRNP complex nucleus ribonucleoprotein complex U2-type catalytic step 2 spliceosome
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 114 kDa -
LEVO
Name: Pre-mRNA-splicing factor PRP46
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [6]
Biological process:
mRNA splicing, via spliceosome

Cellular location:
Cul4-RING E3 ubiquitin ligase complex cytoplasm spliceosomal complex catalytic step 2 spliceosome Prp19 complex
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 50 kDa -
LEVO
Name: Pre-mRNA-processing protein 45
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [5]
Biological process:
generation of catalytic spliceosome for second transesterification step

Cellular location:
U2-type catalytic step 1 spliceosome nucleus post-mRNA release spliceosomal complex U2-type catalytic step 2 spliceosome
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 42 kDa -
LEVO
Name: Pre-mRNA-splicing factor SLT11
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [7]
Biological process:
mRNA splicing, via spliceosome
Molecular function:
U6 snRNA binding pre-mRNA binding
Cellular location:
nucleus U2-type catalytic step 1 spliceosome U2-type catalytic step 2 spliceosome Prp19 complex
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 40 kDa -
LEVO
Name: Pre-mRNA-splicing factor CWC2
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [12]
Biological process:
positive regulation of cell cycle cell cycle mRNA cis splicing, via spliceosome positive regulation of RNA splicing spliceosomal snRNP assembly mRNA splicing, via spliceosome
Molecular function:
pre-mRNA binding U6 snRNA binding metal ion binding
Cellular location:
Prp19 complex U2-type catalytic step 1 spliceosome U2-type catalytic step 2 spliceosome
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 38 kDa -
LEVO
Name: Pre-mRNA-splicing factor CWC15
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [6]
Biological process:
mRNA splicing, via spliceosome mRNA cis splicing, via spliceosome
Molecular function:
RNA binding
Cellular location:
U2-type spliceosomal complex catalytic step 2 spliceosome nucleus
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 19 kDa -
LEVO
Name: Pre-mRNA-splicing factor BUD31
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [5]
Biological process:
mRNA splicing, via spliceosome cellular bud site selection

Cellular location:
spliceosomal complex nucleus U2 snRNP
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 18 kDa -
LEVO
Name: Pre-mRNA-splicing factor CWC21
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [3]
Biological process:
mRNA splicing, via spliceosome

Cellular location:
U2-type spliceosomal complex cytoplasm
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 15 kDa -
LEVO
Name: Pre-mRNA-splicing factor CWC22
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [5]
Biological process:
mRNA splicing, via spliceosome
Molecular function:
RNA binding
Cellular location:
cytoplasm U2-type spliceosomal complex catalytic step 2 spliceosome
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 67 kDa -
LEVO
Name: Pre-mRNA-processing factor Prp17
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 52 kDa -
LEVO
Name: Pre-mRNA-splicing factor Prp18
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 28 kDa -
LEVO
Name: Pre-mRNA-splicing factor SLU7
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [7]
Biological process:
RNA splicing generation of catalytic spliceosome for second transesterification step
Molecular function:
pre-mRNA 3'-splice site binding zinc ion binding second spliceosomal transesterification activity
Cellular location:
U2-type post-spliceosomal complex spliceosomal complex
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 44 kDa -
LEVO
Name: Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP22
EC number: 3.6.4.13
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [9]
Biological process:
spliceosomal complex disassembly generation of catalytic spliceosome for second transesterification step
Molecular function:
RNA helicase activity RNA binding ATP binding ATP hydrolysis activity
Cellular location:
U2-type post-spliceosomal complex catalytic step 2 spliceosome U2-type catalytic step 2 spliceosome
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 130 kDa -
LEVO
Name: Pre-mRNA-splicing factor SYF2
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [8]
Biological process:
mRNA splicing, via spliceosome

Cellular location:
U2-type prespliceosome U2-type catalytic step 2 spliceosome U2-type post-mRNA release spliceosomal complex U2-type catalytic step 1 spliceosome nucleus Prp19 complex cytosol
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 24 kDa -
LEVO
Name: Pre-mRNA-splicing factor CEF1
Number of copies: 1
UniProtKB UniProtKB PDBe-KB PDBe-KB AlphaFold DB AlphaFold DB
Domains
Gene Ontology [7]
Biological process:
generation of catalytic spliceosome for second transesterification step mRNA splicing, via spliceosome
Molecular function:
DNA binding
Cellular location:
U2-type catalytic step 1 spliceosome spliceosomal complex cytoplasm Prp19 complex
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 67 kDa -
LEVO
Name: Pre-mRNA-splicing factor CLF1
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 82 kDa -
LEVO
Name: Pre-mRNA-splicing factor SYF1
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [10]
Biological process:
mRNA splicing, via spliceosome generation of catalytic spliceosome for first transesterification step

Cellular location:
U2-type prespliceosome U2-type catalytic step 2 spliceosome U2-type post-mRNA release spliceosomal complex cytosol Prp19 complex U2-type catalytic step 1 spliceosome nucleus post-mRNA release spliceosomal complex
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 100 kDa -
LEVO
Name: Unknown protein fragment
Number of copies: 1
Natural source
Organism: Saccharomyces cerevisiae
Molecular weight
Experimental Theoretical Method
- 18 kDa -
LEVO
Name: Unknown protein fragment
Number of copies: 1
Natural source
Organism: Saccharomyces cerevisiae
Molecular weight
Experimental Theoretical Method
- 1 kDa -
LEVO
Name: Small nuclear ribonucleoprotein Sm D2
Number of copies: 2
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [22]
Biological process:
U2-type prespliceosome assembly spliceosomal complex assembly mRNA 5'-splice site recognition 7-methylguanosine cap hypermethylation spliceosomal snRNP assembly mRNA splicing, via spliceosome
Molecular function:
RNA binding
Cellular location:
pICln-Sm protein complex nucleus U4/U6 snRNP cytoplasm commitment complex U4 snRNP spliceosomal complex U2-type prespliceosome U1 snRNP U4/U6 x U5 tri-snRNP complex U5 snRNP cytosol U2 snRNP precatalytic spliceosome catalytic step 2 spliceosome
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 12 kDa -
LEVO
Name: Small nuclear ribonucleoprotein F
Number of copies: 2
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [21]
Biological process:
mRNA 5'-splice site recognition U2-type prespliceosome assembly spliceosomal complex assembly spliceosomal snRNP assembly 7-methylguanosine cap hypermethylation mRNA splicing, via spliceosome
Molecular function:
RNA binding poly(U) RNA binding splicing factor binding
Cellular location:
pICln-Sm protein complex U4 snRNP spliceosomal complex commitment complex nucleus U4/U6 snRNP U4/U6 x U5 tri-snRNP complex cytoplasm catalytic step 2 spliceosome U2 snRNP U1 snRNP U5 snRNP
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 9 kDa -
LEVO
Name: Small nuclear ribonucleoprotein E
Number of copies: 2
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [21]
Biological process:
spliceosomal complex assembly U2-type prespliceosome assembly mRNA 5'-splice site recognition 7-methylguanosine cap hypermethylation mRNA splicing, via spliceosome spliceosomal snRNP assembly
Molecular function:
RNA binding splicing factor binding
Cellular location:
pICln-Sm protein complex nucleus commitment complex spliceosomal complex U4/U6 snRNP U2-type prespliceosome U5 snRNP U2 snRNP precatalytic spliceosome U4/U6 x U5 tri-snRNP complex U1 snRNP cytoplasm U4 snRNP
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 10 kDa -
LEVO
Name: Small nuclear ribonucleoprotein G
Number of copies: 2
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [24]
Biological process:
U2-type prespliceosome assembly spliceosomal complex assembly mRNA 5'-splice site recognition 7-methylguanosine cap hypermethylation spliceosomal snRNP assembly mRNA splicing, via spliceosome
Molecular function:
RNA binding
Cellular location:
nucleus spliceosomal complex cytoplasm commitment complex U4/U6 snRNP precatalytic spliceosome catalytic step 2 spliceosome U2-type prespliceosome U4 snRNP U2 snRNP U12-type spliceosomal complex U5 snRNP spliceosomal tri-snRNP complex ribonucleoprotein complex U4/U6 x U5 tri-snRNP complex U1 snRNP SMN-Sm protein complex
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 8 kDa -
LEVO
Name: Small nuclear ribonucleoprotein-associated protein B
Number of copies: 2
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [19]
Biological process:
spliceosomal complex assembly mRNA 5'-splice site recognition U2-type prespliceosome assembly spliceosomal snRNP assembly mRNA splicing, via spliceosome 7-methylguanosine cap hypermethylation
Molecular function:
RNA binding
Cellular location:
nucleus U4/U6 snRNP spliceosomal complex commitment complex U2-type prespliceosome U2 snRNP U5 snRNP U4/U6 x U5 tri-snRNP complex cytoplasm U1 snRNP U4 snRNP catalytic step 2 spliceosome
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 22 kDa -
LEVO
Name: Small nuclear ribonucleoprotein Sm D3
Number of copies: 2
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [26]
Biological process:
U2-type prespliceosome assembly mRNA 5'-splice site recognition spliceosomal complex assembly spliceosomal snRNP assembly mRNA splicing, via spliceosome 7-methylguanosine cap hypermethylation
Molecular function:
RNA binding mRNA binding
Cellular location:
spliceosomal complex U4/U6 snRNP cytoplasm nucleus pICln-Sm protein complex U12-type spliceosomal complex U4/U6 x U5 tri-snRNP complex commitment complex U2 snRNP SMN-Sm protein complex U4 snRNP U1 snRNP cytosol catalytic step 2 spliceosome U5 snRNP precatalytic spliceosome U2-type prespliceosome spliceosomal tri-snRNP complex
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 11 kDa -
LEVO
Name: Small nuclear ribonucleoprotein Sm D1
Number of copies: 2
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [27]
Biological process:
mRNA splicing, via spliceosome U2-type prespliceosome assembly mRNA 5'-splice site recognition spliceosomal complex assembly spliceosomal snRNP assembly 7-methylguanosine cap hypermethylation
Molecular function:
mRNA binding RNA binding
Cellular location:
spliceosomal complex U4/U6 snRNP cytoplasm U2 snRNP pICln-Sm protein complex U1 snRNP U2-type prespliceosome cytosol SMN-Sm protein complex small nuclear ribonucleoprotein complex U5 snRNP spliceosomal tri-snRNP complex nucleus U4 snRNP precatalytic spliceosome commitment complex U4/U6 x U5 tri-snRNP complex U12-type spliceosomal complex catalytic step 2 spliceosome
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 16 kDa -
LEVO
Name: Lea1
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [9]
Biological process:
U2-type prespliceosome assembly mRNA splicing, via spliceosome
Molecular function:
U2 snRNA binding U1 snRNA binding
Cellular location:
spliceosomal complex nucleus U2 snRNP U2-type prespliceosome U1 snRNP
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 12 kDa -
LEVO
Name: Msl1
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [8]
Biological process:
U2-type prespliceosome assembly mRNA splicing, via spliceosome
Molecular function:
U2 snRNA binding
Cellular location:
nucleus spliceosomal complex U2 snRNP U2-type prespliceosome cytoplasm
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 27 kDa -
LEVO
Name: Pre-mRNA-processing factor Prp19
EC number: 2.3.2.27
Number of copies: 4
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [13]
Biological process:
mRNA splicing, via spliceosome generation of catalytic spliceosome for first transesterification step DNA repair protein K63-linked ubiquitination
Molecular function:
ubiquitin protein ligase activity ubiquitin-protein transferase activity identical protein binding
Cellular location:
U2-type catalytic step 1 spliceosome mitochondrion nucleus cytosol cytoplasm Prp19 complex
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 56 kDa -
LEVO
Name: Pre-mRNA-splicing factor SNT309
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Gene Ontology [3]
Biological process:
mRNA splicing, via spliceosome

Cellular location:
U2-type catalytic step 1 spliceosome Prp19 complex
Natural source
Organism: Baker's yeast
Strain: ATCC 204508 / S288c
Molecular weight
Experimental Theoretical Method
- 20 kDa -
Ligand [4]
Name: MAGNESIUM ION
HET code: MG
Number of copies: 5
ChEBI DrugBank
Molecular weight
Experimental Theoretical Method
- 24 Da -
Name: INOSITOL HEXAKISPHOSPHATE
HET code: IHP
Number of copies: 1
ChEMBL ChEBI DrugBank
Molecular weight
Experimental Theoretical Method
- 660 Da -
Name: GUANOSINE-5'-TRIPHOSPHATE
HET code: GTP
Number of copies: 1
ChEMBL ChEBI DrugBank
Molecular weight
Experimental Theoretical Method
- 523 Da -
Name: ZINC ION
HET code: ZN
Number of copies: 7
ChEMBL ChEBI DrugBank
Molecular weight
Experimental Theoretical Method
- 65 Da -