› 3jcm

Electron Microscopy
3.8Å resolution

Cryo-EM structure of the spliceosomal U4/U6.U5 tri-snRNP

Released:
DOI: 10.2210/pdb3jcm/pdb
PDB entry 3jcm coloured by chain, front view.
PDB entry 3jcm coloured by chain, side view.
PDB entry 3jcm coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
The 3.8 Å structure of the U4/U6.U5 tri-snRNP: Insights into spliceosome assembly and catalysis.
Wan R, Yan C, Bai R, Wang L, Huang M, Wong CC, Shi Y
Science 351 466-75 (2016)
PMID: 26743623
Related structures: EMD-6561

Function and Biology Details

Reaction catalysed: 
ATP + H(2)O = ADP + phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 34-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-148702 (preferred)
Entry contents:
23 distinct polypeptide molecules
4 distinct RNA molecules
Macromolecules (27 distinct):
Pre-mRNA-splicing factor 8 Chain: A
Molecule details ›
Chain: A
Length: 2413 amino acids
Theoretical weight: 279.87 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P33334 (Residues: 1-2413; Coverage: 100%)
Gene names: DBF3, DNA39, PRP8, RNA8, SLT21, USA2, YHR165C
Sequence domains:
U4/U6 small nuclear ribonucleoprotein PRP4 Chain: B
Molecule details ›
Chain: B
Length: 465 amino acids
Theoretical weight: 52.51 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P20053 (Residues: 1-465; Coverage: 100%)
Gene names: P9705.6, PRP4, RNA4, YPR178W
Sequence domains: WD domain, G-beta repeat
Pre-mRNA-processing factor 31 Chain: I
Molecule details ›
Chain: I
Length: 494 amino acids
Theoretical weight: 56.38 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P49704 (Residues: 1-494; Coverage: 100%)
Gene names: PRP31, YGR091W
Sequence domains:
Pre-mRNA-splicing factor 6 Chain: G
Molecule details ›
Chain: G
Length: 899 amino acids
Theoretical weight: 104.37 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P19735 (Residues: 1-899; Coverage: 100%)
Gene names: PRP6, RNA6, YBR0508, YBR055C
Sequence domains: PRP1 splicing factor, N-terminal
U4/U6 small nuclear ribonucleoprotein PRP3 Chain: K
Molecule details ›
Chain: K
Length: 469 amino acids
Theoretical weight: 55.97 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q03338 (Residues: 1-469; Coverage: 100%)
Gene names: D8035.16, PRP3, RNA3, YDR473C
Sequence domains:
Spliceosomal protein DIB1 Chain: L
Molecule details ›
Chain: L
Length: 143 amino acids
Theoretical weight: 16.8 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q06819 (Residues: 1-143; Coverage: 100%)
Gene names: CDH1, DIB1, P9513.12, SNU16, YPR082C
Sequence domains: Mitosis protein DIM1
Structure domains: Glutaredoxin
13 kDa ribonucleoprotein-associated protein Chain: M
Molecule details ›
Chain: M
Length: 126 amino acids
Theoretical weight: 13.58 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P39990 (Residues: 1-126; Coverage: 100%)
Gene names: SNU13, YEL026W
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Structure domains: 60s Ribosomal Protein L30; Chain: A;
Pre-mRNA-splicing factor SNU114 Chain: H
Molecule details ›
Chain: H
Length: 1008 amino acids
Theoretical weight: 114.17 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P36048 (Residues: 1-1008; Coverage: 100%)
Gene names: GIN10, SNU114, YKL173W, YKL637
Sequence domains:
Structure domains: Elongation Factor G (Translational Gtpase), domain 3
Pre-mRNA-splicing helicase BRR2 Chain: N
Molecule details ›
Chain: N
Length: 2163 amino acids
Theoretical weight: 246.47 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P32639 (Residues: 1-2163; Coverage: 100%)
Gene names: BRR2, RSS1, SNU246, SYGP-ORF66, YER172C
Sequence domains:
Structure domains:
Small nuclear ribonucleoprotein Sm D3 Chains: J, R
Molecule details ›
Chains: J, R
Length: 101 amino acids
Theoretical weight: 11.24 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P43321 (Residues: 1-101; Coverage: 100%)
Gene names: L9634.6, SMD3, YLR147C
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
Small nuclear ribonucleoprotein-associated protein B Chains: O, S
Molecule details ›
Chains: O, S
Length: 196 amino acids
Theoretical weight: 22.43 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P40018 (Residues: 1-196; Coverage: 100%)
Gene names: SMB1, YER029C
Sequence domains: LSM domain
Small nuclear ribonucleoprotein Sm D1 Chains: P, T
Molecule details ›
Chains: P, T
Length: 146 amino acids
Theoretical weight: 16.3 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q02260 (Residues: 1-146; Coverage: 100%)
Gene names: SMD1, YGR074W
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
Small nuclear ribonucleoprotein Sm D2 Chains: Q, U
Molecule details ›
Chains: Q, U
Length: 110 amino acids
Theoretical weight: 12.88 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q06217 (Residues: 1-110; Coverage: 100%)
Gene names: L9328.5, SMD2, YLR275W
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
Small nuclear ribonucleoprotein E Chains: V, Y
Molecule details ›
Chains: V, Y
Length: 94 amino acids
Theoretical weight: 10.39 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q12330 (Residues: 1-94; Coverage: 100%)
Gene names: SME1, YOR159C
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
Small nuclear ribonucleoprotein F Chains: W, Z
Molecule details ›
Chains: W, Z
Length: 86 amino acids
Theoretical weight: 9.67 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P54999 (Residues: 1-86; Coverage: 100%)
Gene names: P9705.4, SMX3, YPR182W
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
Small nuclear ribonucleoprotein G Chains: X, a
Molecule details ›
Chains: X, a
Length: 77 amino acids
Theoretical weight: 8.49 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P40204 (Residues: 1-77; Coverage: 100%)
Gene names: SMX2, SNP2, YFL017Bw, YFL017W-A
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
U6 snRNA-associated Sm-like protein LSm8 Chain: b
Molecule details ›
Chain: b
Length: 109 amino acids
Theoretical weight: 12.4 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P47093 (Residues: 1-109; Coverage: 100%)
Gene names: J1464, LSM8, YJR022W, YJR83.16
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
U6 snRNA-associated Sm-like protein LSm2 Chain: c
Molecule details ›
Chain: c
Length: 95 amino acids
Theoretical weight: 11.18 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P38203 (Residues: 1-95; Coverage: 100%)
Gene names: LSM2, SMX5, SNP3, YBL026W, YBL0425
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
U6 snRNA-associated Sm-like protein LSm3 Chain: d
Molecule details ›
Chain: d
Length: 89 amino acids
Theoretical weight: 10.04 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P57743 (Residues: 1-89; Coverage: 100%)
Gene names: LSM3, SMX4, USS2, YLR438C-A
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
U6 snRNA-associated Sm-like protein LSm6 Chain: e
Molecule details ›
Chain: e
Length: 86 amino acids
Theoretical weight: 9.41 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q06406 (Residues: 1-86; Coverage: 100%)
Gene names: D9481.18, LSM6, YDR378C
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
U6 snRNA-associated Sm-like protein LSm5 Chain: f
Molecule details ›
Chain: f
Length: 93 amino acids
Theoretical weight: 10.43 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P40089 (Residues: 1-93; Coverage: 100%)
Gene names: LSM5, YER146W
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
U6 snRNA-associated Sm-like protein LSm7 Chain: g
Molecule details ›
Chain: g
Length: 115 amino acids
Theoretical weight: 13.03 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P53905 (Residues: 1-115; Coverage: 100%)
Gene names: LSM7, N1202, N1780, YNL147W
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
U6 snRNA-associated Sm-like protein LSm4 Chain: h
Molecule details ›
Chain: h
Length: 187 amino acids
Theoretical weight: 21.3 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P40070 (Residues: 1-187; Coverage: 100%)
Gene names: LSM4, SDB23, USS1, YER112W
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
pre-mRNA Chain: C
Molecule details ›
Chain: C
Length: 20 nucleotides
Theoretical weight: 6.43 KDa
SNR6 snRNA Chain: D
Molecule details ›
Chain: D
Length: 112 nucleotides
Theoretical weight: 35.88 KDa
Sequence domains: U6 spliceosomal RNA
SNR14 snRNA Chain: E
Molecule details ›
Chain: E
Length: 160 nucleotides
Theoretical weight: 51.19 KDa
Sequence domains: U4 spliceosomal RNA
SNR7-L snRNA Chain: F
Molecule details ›
Chain: F
Length: 214 nucleotides
Theoretical weight: 68.64 KDa
Sequence domains: U5 spliceosomal RNA

Ligands and Environments

2 bound ligands:
Ligand GTP 1 x GTP
Ligand M7M 1 x M7M
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.8Å
Relevant EMDB volumes: EMD-6561

Quick links

Citations

42 review citations

Therapeutic targeting of splicing in cancer.
Lee et al. (2016)
41 more

7 mentions without citation

RNAs in the spliceosome: Insight from cryoEM structures.
Zhang et al. (2019)
6 more