EMD-8012

Single-particle
3.7 Å
EMD-8012
3D View Gallery
Deposition: 15/12/2015
Map released: 27/01/2016
Last modified: 11/12/2019
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Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-8012
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EMICSS annotations (xml)

The overall structure of the yeast spliceosomal U4/U6.U5 tri-snRNP at 3.7 Angstrom

EMD-8012

Single-particle
3.7 Å
EMD-8012
3D View Gallery
Deposition: 15/12/2015
Map released: 27/01/2016
Last modified: 11/12/2019
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Name: The overall structure of the yeast spliceosomal U4/U6.U5 tri-snRNP
Complex [1]
Name: The overall structure of the yeast spliceosomal U4/U6.U5 tri-snRNP
Details: 30 proteins and 3 snRNAs
Natural source [1]
Organism: Saccharomyces cerevisiae
Strain: BCY123
Molecular weight
Experimental Theoretical Method
- 1 MDa -
Complex Portal [1]
ID Name Overlap
CPX-25 U4/U6.U5 tri-small nuclear ribonucleoprotein complex 0.79
RNA [3]
Name: U4 snRNA
Number of copies: 1
Natural source
Organism: Baker's yeast
Strain: BCY123
Molecular weight
Experimental Theoretical Method
- 51 kDa -
Name: U6 snRNA
Number of copies: 1
Natural source
Organism: Baker's yeast
Strain: BCY123
Molecular weight
Experimental Theoretical Method
- 35 kDa -
Name: U5 snRNA
Number of copies: 1
Natural source
Organism: Baker's yeast
Strain: BCY123
Molecular weight
Experimental Theoretical Method
- 68 kDa -
Protein [25]
LEVO
Name: Pre-mRNA-splicing factor 8
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 spliceosomal tri-snRNP complex assembly generation of catalytic spliceosome for second transesterification step
Molecular function:
metallopeptidase activity U6 snRNA binding U2 snRNA binding U5 snRNA binding U1 snRNA binding isopeptidase activity pre-mRNA intronic binding mRNA binding
Cellular location:
cytoplasm spliceosomal complex catalytic step 2 spliceosome U4/U6 x U5 tri-snRNP complex U5 snRNP nucleus
Natural source
Organism: Baker's yeast
Strain: BCY123
Molecular weight
Experimental Theoretical Method
- 279 kDa -
LEVO
Name: U4/U6 small nuclear ribonucleoprotein PRP4
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [11]
Biological process:
spliceosomal complex assembly snoRNA splicing mRNA splicing, via spliceosome spliceosomal conformational changes to generate catalytic conformation
Molecular function:
U4 snRNA binding U6 snRNA binding
Cellular location:
U4 snRNP nucleus U4/U6 snRNP U4/U6 x U5 tri-snRNP complex spliceosomal complex
Natural source
Organism: Baker's yeast
Strain: BCY123
Molecular weight
Experimental Theoretical Method
- 52 kDa -
LEVO
Name: Pre-mRNA-splicing factor 6
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [8]
Biological process:
mRNA splicing, via spliceosome spliceosomal tri-snRNP complex assembly

Cellular location:
U5 snRNP nucleus spliceosomal complex U4/U6 x U5 tri-snRNP complex U4/U6 snRNP catalytic step 2 spliceosome
Natural source
Organism: Baker's yeast
Strain: BCY123
Molecular weight
Experimental Theoretical Method
- 104 kDa -
LEVO
Name: Spliceosomal protein DIB1
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [5]
Biological process:
mRNA splicing, via spliceosome

Cellular location:
nucleus U5 snRNP U4/U6 x U5 tri-snRNP complex spliceosomal complex
Natural source
Organism: Baker's yeast
Strain: BCY123
Molecular weight
Experimental Theoretical Method
- 16 kDa -
LEVO
Name: Pre-mRNA-processing factor 31
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [12]
Biological process:
spliceosomal tri-snRNP complex assembly spliceosomal snRNP assembly mRNA splicing, via spliceosome
Molecular function:
RNA binding
Cellular location:
U4/U6 snRNP spliceosomal complex nucleus spliceosomal tri-snRNP complex precatalytic spliceosome U4 snRNP U4/U6 x U5 tri-snRNP complex mitochondrion
Natural source
Organism: Baker's yeast
Strain: BCY123
Molecular weight
Experimental Theoretical Method
- 56 kDa -
LEVO
Name: U4/U6 small nuclear ribonucleoprotein PRP3
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [8]
Biological process:
spliceosomal complex assembly spliceosomal snRNP assembly mRNA splicing, via spliceosome

Cellular location:
U4/U6 snRNP U4 snRNP nucleus spliceosomal complex U4/U6 x U5 tri-snRNP complex
Natural source
Organism: Baker's yeast
Strain: BCY123
Molecular weight
Experimental Theoretical Method
- 55 kDa -
LEVO
Name: Pre-mRNA-splicing helicase BRR2
EC number: 3.6.4.13
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [11]
Biological process:
mRNA splicing, via spliceosome spliceosome conformational change to release U4 (or U4atac) and U1 (or U11)
Molecular function:
RNA helicase activity ATP hydrolysis activity identical protein binding nucleic acid binding ATP binding
Cellular location:
spliceosomal complex U4/U6 x U5 tri-snRNP complex U5 snRNP nucleus
Natural source
Organism: Baker's yeast
Strain: BCY123
Molecular weight
Experimental Theoretical Method
- 246 kDa -
LEVO
Name: Unknown protein
Number of copies: 1
Natural source
Organism: Baker's yeast
Strain: BCY123
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:
mRNA 5'-splice site recognition spliceosomal complex assembly spliceosomal snRNP assembly U2-type prespliceosome assembly 7-methylguanosine cap hypermethylation mRNA splicing, via spliceosome
Molecular function:
RNA binding
Cellular location:
spliceosomal complex commitment complex U4/U6 snRNP nucleus U1 snRNP U2 snRNP U4/U6 x U5 tri-snRNP complex cytoplasm catalytic step 2 spliceosome U4 snRNP U5 snRNP U2-type prespliceosome
Natural source
Organism: Baker's yeast
Strain: BCY123
Molecular weight
Experimental Theoretical Method
- 22 kDa -
LEVO
Name: Small nuclear ribonucleoprotein Sm D1
Number of copies: 2
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [27]
Biological process:
U2-type prespliceosome assembly spliceosomal complex assembly mRNA 5'-splice site recognition spliceosomal snRNP assembly mRNA splicing, via spliceosome 7-methylguanosine cap hypermethylation
Molecular function:
RNA binding mRNA binding
Cellular location:
U4/U6 snRNP cytoplasm spliceosomal complex nucleus pICln-Sm protein complex U5 snRNP spliceosomal tri-snRNP complex cytosol U1 snRNP U4/U6 x U5 tri-snRNP complex small nuclear ribonucleoprotein complex precatalytic spliceosome U2-type prespliceosome SMN-Sm protein complex U12-type spliceosomal complex catalytic step 2 spliceosome U4 snRNP commitment complex U2 snRNP
Natural source
Organism: Baker's yeast
Strain: BCY123
Molecular weight
Experimental Theoretical Method
- 16 kDa -
LEVO
Name: Small nuclear ribonucleoprotein Sm D2
Number of copies: 2
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [22]
Biological process:
mRNA 5'-splice site recognition spliceosomal complex assembly U2-type prespliceosome assembly mRNA splicing, via spliceosome spliceosomal snRNP assembly 7-methylguanosine cap hypermethylation
Molecular function:
RNA binding
Cellular location:
pICln-Sm protein complex commitment complex cytoplasm U4/U6 snRNP nucleus U4 snRNP spliceosomal complex U1 snRNP catalytic step 2 spliceosome U2 snRNP U4/U6 x U5 tri-snRNP complex U5 snRNP cytosol precatalytic spliceosome U2-type prespliceosome
Natural source
Organism: Baker's yeast
Strain: BCY123
Molecular weight
Experimental Theoretical Method
- 12 kDa -
LEVO
Name: Small nuclear ribonucleoprotein Sm D3
Number of copies: 2
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [26]
Biological process:
mRNA 5'-splice site recognition spliceosomal complex assembly U2-type prespliceosome assembly 7-methylguanosine cap hypermethylation spliceosomal snRNP assembly mRNA splicing, via spliceosome
Molecular function:
RNA binding mRNA binding
Cellular location:
cytoplasm nucleus spliceosomal complex U4/U6 snRNP U12-type spliceosomal complex SMN-Sm protein complex spliceosomal tri-snRNP complex U2-type prespliceosome U1 snRNP U4 snRNP precatalytic spliceosome catalytic step 2 spliceosome pICln-Sm protein complex commitment complex U4/U6 x U5 tri-snRNP complex U2 snRNP cytosol U5 snRNP
Natural source
Organism: Baker's yeast
Strain: BCY123
Molecular weight
Experimental Theoretical Method
- 11 kDa -
LEVO
Name: Small nuclear ribonucleoprotein E
Number of copies: 2
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [21]
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:
splicing factor binding RNA binding
Cellular location:
pICln-Sm protein complex U4/U6 snRNP nucleus commitment complex spliceosomal complex U4 snRNP U1 snRNP U2 snRNP cytoplasm U2-type prespliceosome U5 snRNP precatalytic spliceosome U4/U6 x U5 tri-snRNP complex
Natural source
Organism: Baker's yeast
Strain: BCY123
Molecular weight
Experimental Theoretical Method
- 10 kDa -
LEVO
Name: Small nuclear ribonucleoprotein F
Number of copies: 2
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [21]
Biological process:
U2-type prespliceosome assembly spliceosomal complex assembly mRNA 5'-splice site recognition spliceosomal snRNP assembly 7-methylguanosine cap hypermethylation mRNA splicing, via spliceosome
Molecular function:
splicing factor binding poly(U) RNA binding RNA binding
Cellular location:
pICln-Sm protein complex U4 snRNP commitment complex nucleus U4/U6 snRNP spliceosomal complex U1 snRNP U2 snRNP U4/U6 x U5 tri-snRNP complex U5 snRNP catalytic step 2 spliceosome cytoplasm
Natural source
Organism: Baker's yeast
Strain: BCY123
Molecular weight
Experimental Theoretical Method
- 9 kDa -
LEVO
Name: Small nuclear ribonucleoprotein G
Number of copies: 2
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [24]
Biological process:
spliceosomal complex assembly U2-type prespliceosome assembly mRNA 5'-splice site recognition mRNA splicing, via spliceosome spliceosomal snRNP assembly 7-methylguanosine cap hypermethylation
Molecular function:
RNA binding
Cellular location:
commitment complex nucleus U4/U6 snRNP spliceosomal complex cytoplasm U1 snRNP U12-type spliceosomal complex ribonucleoprotein complex catalytic step 2 spliceosome U4/U6 x U5 tri-snRNP complex U5 snRNP SMN-Sm protein complex spliceosomal tri-snRNP complex U2 snRNP U4 snRNP U2-type prespliceosome precatalytic spliceosome
Natural source
Organism: Baker's yeast
Strain: BCY123
Molecular weight
Experimental Theoretical Method
- 8 kDa -
LEVO
Name: Snu66
Number of copies: 1
Details: Snu66 is mostly fitted as polyAla into helices and extended polypeptides within the EM map. The authors do not believe that the sequence number is correct.
Natural source
Organism: Baker's yeast
Strain: BCY123
Molecular weight
Experimental Theoretical Method
- 28 kDa -
LEVO
Name: 13 kDa ribonucleoprotein-associated protein
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [22]
Biological process:
spliceosomal complex assembly snoRNA guided rRNA 2'-O-methylation maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) positive regulation of RNA binding box C/D RNA 3'-end processing maturation of LSU-rRNA maturation of SSU-rRNA mRNA splicing, via spliceosome
Molecular function:
RNA binding U3 snoRNA binding U4 snRNA binding
Cellular location:
cytosolic large ribosomal subunit U4 snRNP U4/U6 snRNP nucleus spliceosomal complex nucleoplasm small-subunit processome precatalytic spliceosome box C/D RNP complex U4/U6 x U5 tri-snRNP complex nucleolus
Natural source
Organism: Baker's yeast
Strain: BCY123
Molecular weight
Experimental Theoretical Method
- 13 kDa -
LEVO
Name: U6 snRNA-associated Sm-like protein LSm2
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [17]
Biological process:
rRNA processing mRNA splicing, via spliceosome tRNA processing deadenylation-dependent decapping of nuclear-transcribed mRNA
Molecular function:
RNA binding
Cellular location:
spliceosomal complex U4/U6 snRNP Lsm1-7-Pat1 complex catalytic step 2 spliceosome nucleolus P-body U4/U6 x U5 tri-snRNP complex cytoplasm sno(s)RNA-containing ribonucleoprotein complex U6 snRNP nucleus precatalytic spliceosome
Natural source
Organism: Baker's yeast
Strain: BCY123
Molecular weight
Experimental Theoretical Method
- 11 kDa -
LEVO
Name: U6 snRNA-associated Sm-like protein LSm3
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [18]
Biological process:
tRNA processing deadenylation-dependent decapping of nuclear-transcribed mRNA mRNA splicing, via spliceosome P-body assembly rRNA processing
Molecular function:
RNA binding
Cellular location:
U4/U6 snRNP spliceosomal complex nucleus P-body catalytic step 2 spliceosome sno(s)RNA-containing ribonucleoprotein complex U6 snRNP nucleolus U4/U6 x U5 tri-snRNP complex cytoplasm precatalytic spliceosome Lsm1-7-Pat1 complex
Natural source
Organism: Baker's yeast
Strain: BCY123
Molecular weight
Experimental Theoretical Method
- 10 kDa -
LEVO
Name: U6 snRNA-associated Sm-like protein LSm4
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [19]
Biological process:
P-body assembly spliceosomal snRNP assembly mRNA splicing, via spliceosome tRNA processing rRNA processing deadenylation-dependent decapping of nuclear-transcribed mRNA
Molecular function:
RNA binding U6 snRNA binding
Cellular location:
U4/U6 snRNP Lsm1-7-Pat1 complex cytoplasm spliceosomal tri-snRNP complex nucleolus U6 snRNP sno(s)RNA-containing ribonucleoprotein complex U4/U6 x U5 tri-snRNP complex spliceosomal complex P-body nucleus
Natural source
Organism: Baker's yeast
Strain: BCY123
Molecular weight
Experimental Theoretical Method
- 21 kDa -
LEVO
Name: U6 snRNA-associated Sm-like protein LSm5
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [15]
Biological process:
tRNA processing mRNA splicing, via spliceosome nuclear-transcribed mRNA catabolic process deadenylation-dependent decapping of nuclear-transcribed mRNA rRNA processing
Molecular function:
RNA binding
Cellular location:
U4/U6 snRNP P-body nucleolus U4/U6 x U5 tri-snRNP complex Lsm1-7-Pat1 complex U6 snRNP nucleus spliceosomal complex sno(s)RNA-containing ribonucleoprotein complex
Natural source
Organism: Baker's yeast
Strain: BCY123
Molecular weight
Experimental Theoretical Method
- 10 kDa -
LEVO
Name: U6 snRNA-associated Sm-like protein LSm6
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [15]
Biological process:
deadenylation-dependent decapping of nuclear-transcribed mRNA mRNA splicing, via spliceosome tRNA processing maturation of SSU-rRNA rRNA processing
Molecular function:
RNA binding
Cellular location:
U4/U6 snRNP spliceosomal complex P-body U6 snRNP U4/U6 x U5 tri-snRNP complex sno(s)RNA-containing ribonucleoprotein complex Lsm1-7-Pat1 complex nucleus nucleolus
Natural source
Organism: Baker's yeast
Strain: BCY123
Molecular weight
Experimental Theoretical Method
- 9 kDa -
LEVO
Name: U6 snRNA-associated Sm-like protein LSm7
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [22]
Biological process:
mRNA splicing, via spliceosome maturation of SSU-rRNA tRNA processing deadenylation-dependent decapping of nuclear-transcribed mRNA nuclear-transcribed mRNA catabolic process rRNA processing
Molecular function:
RNA binding
Cellular location:
U4/U6 snRNP spliceosomal complex U2-type prespliceosome cytoplasm Lsm1-7-Pat1 complex nucleolus ribonucleoprotein complex nucleus catalytic step 2 spliceosome U4/U6 x U5 tri-snRNP complex P-body spliceosomal tri-snRNP complex U6 snRNP U12-type spliceosomal complex sno(s)RNA-containing ribonucleoprotein complex
Natural source
Organism: Baker's yeast
Strain: BCY123
Molecular weight
Experimental Theoretical Method
- 13 kDa -
LEVO
Name: U6 snRNA-associated Sm-like protein LSm8
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [13]
Biological process:
rRNA processing RNA metabolic process mRNA splicing, via spliceosome tRNA processing
Molecular function:
RNA binding
Cellular location:
U4/U6 snRNP spliceosomal complex U4/U6 x U5 tri-snRNP complex precatalytic spliceosome U6 snRNP nucleolus cytoplasm nucleus
Natural source
Organism: Baker's yeast
Strain: BCY123
Molecular weight
Experimental Theoretical Method
- 12 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 generation of catalytic spliceosome for first transesterification step spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) spliceosomal tri-snRNP complex assembly mRNA splicing, via spliceosome
Molecular function:
translation elongation factor activity U5 snRNA binding GTPase activity GTP binding
Cellular location:
cytosol spliceosomal complex cytoplasm nucleus U5 snRNP U4/U6 x U5 tri-snRNP complex U2-type catalytic step 2 spliceosome ribonucleoprotein complex
Natural source
Organism: Baker's yeast
Strain: BCY123
Molecular weight
Experimental Theoretical Method
- 114 kDa -
Ligand [1]
Name: GUANOSINE-5'-TRIPHOSPHATE
HET code: GTP
Number of copies: 1
ChEMBL ChEBI DrugBank
Molecular weight
Experimental Theoretical Method
- 523 Da -