› 5gan

Electron Microscopy
3.6Å resolution

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

Released:
DOI: 10.2210/pdb5gan/pdb
PDB entry 5gan coloured by chain, front view.
PDB entry 5gan coloured by chain, side view.
PDB entry 5gan coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Cryo-EM structure of the yeast U4/U6.U5 tri-snRNP at 3.7 Å resolution.
Nguyen THD, Galej WP, Bai XC, Oubridge C, Newman AJ, Scheres SHW, Nagai K
Nature 530 298-302 (2016)
PMID: 26829225
Related structures: EMD-8012

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 35-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-148701 (preferred)
Entry contents:
25 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (28 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
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: H
Molecule details ›
Chain: H
Length: 465 amino acids
Theoretical weight: 52.51 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P20053 (Residues: 1-465; Coverage: 100%)
Gene names: P9705.6, PRP4, RNA4, YPR178W
Sequence domains: WD domain, G-beta repeat
Pre-mRNA-splicing factor 6 Chain: J
Molecule details ›
Chain: J
Length: 899 amino acids
Theoretical weight: 104.37 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P19735 (Residues: 1-899; Coverage: 100%)
Gene names: PRP6, RNA6, YBR0508, YBR055C
Sequence domains: PRP1 splicing factor, N-terminal
Spliceosomal protein DIB1 Chain: D
Molecule details ›
Chain: D
Length: 143 amino acids
Theoretical weight: 16.8 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q06819 (Residues: 1-143; Coverage: 100%)
Gene names: CDH1, DIB1, P9513.12, SNU16, YPR082C
Sequence domains: Mitosis protein DIM1
Structure domains: Glutaredoxin
Pre-mRNA-processing factor 31 Chain: F
Molecule details ›
Chain: F
Length: 494 amino acids
Theoretical weight: 56.38 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P49704 (Residues: 1-494; Coverage: 100%)
Gene names: PRP31, YGR091W
Sequence domains:
U4/U6 small nuclear ribonucleoprotein PRP3 Chain: G
Molecule details ›
Chain: G
Length: 469 amino acids
Theoretical weight: 55.97 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q03338 (Residues: 1-469; Coverage: 100%)
Gene names: D8035.16, PRP3, RNA3, YDR473C
Sequence domains:
Pre-mRNA-splicing helicase BRR2 Chain: B
Molecule details ›
Chain: B
Length: 2163 amino acids
Theoretical weight: 246.47 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P32639 (Residues: 1-2163; Coverage: 100%)
Gene names: BRR2, RSS1, SNU246, SYGP-ORF66, YER172C
Sequence domains:
Structure domains:
Unknown protein Chain: x
Molecule details ›
Chain: x
Length: 100 amino acids
Theoretical weight: 8.53 KDa
Source organism: Saccharomyces cerevisiae
Small nuclear ribonucleoprotein-associated protein B Chains: b, k
Molecule details ›
Chains: b, k
Length: 196 amino acids
Theoretical weight: 22.43 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P40018 (Residues: 1-196; Coverage: 100%)
Gene names: SMB1, YER029C
Sequence domains: LSM domain
Small nuclear ribonucleoprotein Sm D1 Chains: h, l
Molecule details ›
Chains: h, l
Length: 146 amino acids
Theoretical weight: 16.3 KDa
Source organism: Saccharomyces cerevisiae
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: j, m
Molecule details ›
Chains: j, m
Length: 110 amino acids
Theoretical weight: 12.88 KDa
Source organism: Saccharomyces cerevisiae
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 Sm D3 Chains: d, n
Molecule details ›
Chains: d, n
Length: 101 amino acids
Theoretical weight: 11.24 KDa
Source organism: Saccharomyces cerevisiae
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 E Chains: e, p
Molecule details ›
Chains: e, p
Length: 94 amino acids
Theoretical weight: 10.39 KDa
Source organism: Saccharomyces cerevisiae
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: f, q
Molecule details ›
Chains: f, q
Length: 86 amino acids
Theoretical weight: 9.67 KDa
Source organism: Saccharomyces cerevisiae
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: g, r
Molecule details ›
Chains: g, r
Length: 77 amino acids
Theoretical weight: 8.49 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P40204 (Residues: 1-77; Coverage: 100%)
Gene names: SMX2, SNP2, YFL017Bw, YFL017W-A
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
66 kDa U4/U6.U5 small nuclear ribonucleoprotein component Chain: E
Molecule details ›
Chain: E
Length: 328 amino acids
Theoretical weight: 28.66 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q12420 (Residues: 540-560; Coverage: 4%)
Gene names: 05667, SNU66, YOR308C
13 kDa ribonucleoprotein-associated protein Chain: K
Molecule details ›
Chain: K
Length: 126 amino acids
Theoretical weight: 13.58 KDa
Source organism: Saccharomyces cerevisiae
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;
U6 snRNA-associated Sm-like protein LSm2 Chain: 2
Molecule details ›
Chain: 2
Length: 95 amino acids
Theoretical weight: 11.18 KDa
Source organism: Saccharomyces cerevisiae
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: 3
Molecule details ›
Chain: 3
Length: 89 amino acids
Theoretical weight: 10.04 KDa
Source organism: Saccharomyces cerevisiae
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 LSm4 Chain: 4
Molecule details ›
Chain: 4
Length: 187 amino acids
Theoretical weight: 21.3 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P40070 (Residues: 1-187; Coverage: 100%)
Gene names: LSM4, SDB23, USS1, YER112W
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
U6 snRNA-associated Sm-like protein LSm5 Chain: 5
Molecule details ›
Chain: 5
Length: 93 amino acids
Theoretical weight: 10.43 KDa
Source organism: Saccharomyces cerevisiae
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 LSm6 Chain: 6
Molecule details ›
Chain: 6
Length: 86 amino acids
Theoretical weight: 9.41 KDa
Source organism: Saccharomyces cerevisiae
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 LSm7 Chain: 7
Molecule details ›
Chain: 7
Length: 115 amino acids
Theoretical weight: 13.03 KDa
Source organism: Saccharomyces cerevisiae
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 LSm8 Chain: 8
Molecule details ›
Chain: 8
Length: 109 amino acids
Theoretical weight: 12.4 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P47093 (Residues: 1-109; Coverage: 100%)
Gene names: J1464, LSM8, YJR022W, YJR83.16
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
Pre-mRNA-splicing factor SNU114 Chain: C
Molecule details ›
Chain: C
Length: 1008 amino acids
Theoretical weight: 114.13 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P36048 (Residues: 1-1008; Coverage: 100%)
Gene names: GIN10, SNU114, YKL173W, YKL637
Sequence domains:
U4 snRNA Chain: V
Molecule details ›
Chain: V
Length: 160 nucleotides
Theoretical weight: 51.19 KDa
Sequence domains: U4 spliceosomal RNA
U6 snRNA Chain: W
Molecule details ›
Chain: W
Length: 112 nucleotides
Theoretical weight: 35.88 KDa
Sequence domains: U6 spliceosomal RNA
U5 snRNA Chain: U
Molecule details ›
Chain: U
Length: 214 nucleotides
Theoretical weight: 68.64 KDa
Sequence domains: U5 spliceosomal RNA

Ligands and Environments

1 bound ligand:
Ligand GTP 1 x GTP
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.6Å
Relevant EMDB volumes: EMD-8012

Quick links

Citations

43 review citations

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

20 mentions without citation

Cryo-electron microscopy snapshots of the spliceosome: structural insights into a dynamic ribonucleoprotein machine.
Fica et al. (2017)
19 more