› 5lj3

Electron Microscopy
3.8Å resolution

Structure of the core of the yeast spliceosome immediately after branching

Released:
DOI: 10.2210/pdb5lj3/pdb
PDB entry 5lj3 coloured by chain, front view.
PDB entry 5lj3 coloured by chain, side view.
PDB entry 5lj3 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Cryo-EM structure of the spliceosome immediately after branching.
Galej WP, Wilkinson ME, Fica SM, Oubridge C, Newman AJ, Nagai K
Nature 537 197-201 (2016)
PMID: 27459055
Related structures: EMD-4055

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 38-mer (preferred)
PDBe Complex ID:
PDB-CPX-149221 (preferred)
Entry contents:
26 distinct polypeptide molecules
5 distinct RNA molecules
Macromolecules (31 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:
Splicing factor YJU2 Chain: D
Molecule details ›
Chain: D
Length: 278 amino acids
Theoretical weight: 32.37 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P28320 (Residues: 1-278; Coverage: 100%)
Gene names: CWC16, YJU2, YKL095W, YKL442
Sequence domains: Saf4/Yju2 protein
Pre-mRNA-splicing factor CWC25 Chain: F
Molecule details ›
Chain: F
Length: 179 amino acids
Theoretical weight: 20.41 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P53854 (Residues: 1-179; Coverage: 100%)
Gene names: CWC25, N0901, YNL245C
Sequence domains:
Pre-mRNA-splicing factor SNU114 Chain: C
Molecule details ›
Chain: C
Length: 1008 amino acids
Theoretical weight: 114.17 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P36048 (Residues: 1-1008; Coverage: 100%)
Gene names: GIN10, SNU114, YKL173W, YKL637
Sequence domains:
Pre-mRNA-splicing factor ISY1 Chain: G
Molecule details ›
Chain: G
Length: 235 amino acids
Theoretical weight: 28.12 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P21374 (Residues: 1-235; Coverage: 100%)
Gene names: ISY1, J1657, NTC30, UTR3, YJR050W
Sequence domains: Isy1-like splicing family
CWC22 Chain: H
Molecule details ›
Chain: H
Length: 591 amino acids
Theoretical weight: 69.12 KDa
Source organism: Saccharomyces cerevisiae
Pre-mRNA-splicing factor PRP46 Chain: J
Molecule details ›
Chain: J
Length: 451 amino acids
Theoretical weight: 50.8 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q12417 (Residues: 1-451; Coverage: 100%)
Gene names: CWC1, NTC50, P2594, PRP46, YPL151C
Sequence domains: WD domain, G-beta repeat
Structure domains: YVTN repeat-like/Quinoprotein amine dehydrogenase
Pre-mRNA-processing protein 45 Chain: K
Molecule details ›
Chain: K
Length: 379 amino acids
Theoretical weight: 42.55 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P28004 (Residues: 1-379; Coverage: 100%)
Gene names: FUN20, PRP45, YAL032C
Sequence domains: SKIP/SNW domain
Pre-mRNA-splicing factor BUD31 Chain: L
Molecule details ›
Chain: L
Length: 157 amino acids
Theoretical weight: 18.48 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P25337 (Residues: 1-157; Coverage: 100%)
Gene names: BUD31, CWC14, YCR063W, YCR63W, YCR903
Sequence domains: Pre-mRNA-splicing factor BUD31
Pre-mRNA-splicing factor CWC2 Chain: M
Molecule details ›
Chain: M
Length: 339 amino acids
Theoretical weight: 38.46 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q12046 (Residues: 1-339; Coverage: 100%)
Gene names: CWC2, D1041, NTC40, SLC3, YDL209C
Sequence domains:
Pre-mRNA-splicing factor SLT11 Chain: N
Molecule details ›
Chain: N
Length: 364 amino acids
Theoretical weight: 40.99 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P38241 (Residues: 1-364; Coverage: 100%)
Gene names: ECM2, SLT11, YBR0614, YBR065C
Sequence domains: STL11, N-terminal
Pre-mRNA-splicing factor CEF1 Chain: O
Molecule details ›
Chain: O
Length: 590 amino acids
Theoretical weight: 67.82 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q03654 (Residues: 1-590; Coverage: 100%)
Gene names: CEF1, NTC85, YM8261.07, YMR213W
Sequence domains:
Pre-mRNA-splicing factor CWC15 Chain: P
Molecule details ›
Chain: P
Length: 175 amino acids
Theoretical weight: 19.97 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q03772 (Residues: 1-175; Coverage: 100%)
Gene names: CWC15, YD8358.17, YDR163W
Sequence domains: Cwf15/Cwc15 cell cycle control protein
Pre-mRNA-splicing factor CWC21 Chain: R
Molecule details ›
Chain: R
Length: 135 amino acids
Theoretical weight: 15.79 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q03375 (Residues: 1-135; Coverage: 100%)
Gene names: CWC21, YDR482C
Sequence domains: cwf21 domain
Pre-mRNA-splicing factor CLF1 Chain: S
Molecule details ›
Chain: S
Length: 687 amino acids
Theoretical weight: 82.53 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q12309 (Residues: 1-687; Coverage: 100%)
Gene names: CLF1, L2952, NTC77, SYF3, YLR117C
Sequence domains: HAT (Half-A-TPR) repeat
Pre-mRNA-splicing factor SYF1 Chain: T
Molecule details ›
Chain: T
Length: 859 amino acids
Theoretical weight: 100.36 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q04048 (Residues: 1-859; Coverage: 100%)
Gene names: NTC90, SYF1, YDR416W
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 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.
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.
U2 small nuclear ribonucleoprotein A' Chain: W
Molecule details ›
Chain: W
Length: 238 amino acids
Theoretical weight: 27.23 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q08963 (Residues: 1-238; Coverage: 100%)
Gene names: LEA1, YPL213W
Sequence domains: Leucine-rich repeat
U2 small nuclear ribonucleoprotein B'' Chain: Y
Molecule details ›
Chain: Y
Length: 111 amino acids
Theoretical weight: 12.85 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P40567 (Residues: 1-111; Coverage: 100%)
Gene names: MSL1, YIB9W, YIR009W
Sequence domains: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
Structure domains: Alpha-Beta Plaits
unknown Chain: x
Molecule details ›
Chain: x
Length: 132 amino acids
Theoretical weight: 11.25 KDa
Source organism: Saccharomyces cerevisiae
U5 snRNA (small nuclear RNA) Chain: U
Molecule details ›
Chain: U
Length: 179 nucleotides
Theoretical weight: 57.44 KDa
Sequence domains: U5 spliceosomal RNA
Exon 1 (5' exon) of UBC4 pre-mRNA Chain: E
Molecule details ›
Chain: E
Length: 16 nucleotides
Theoretical weight: 5.17 KDa
Intron of UBC4 pre-mRNA Chain: I
Molecule details ›
Chain: I
Length: 76 nucleotides
Theoretical weight: 24.11 KDa
U2 snRNA (small nuclear RNA) Chain: Z
Molecule details ›
Chain: Z
Length: 1175 nucleotides
Theoretical weight: 376.27 KDa
Sequence domains: U2 spliceosomal RNA
U6 snRNA (small nuclear RNA) Chain: V
Molecule details ›
Chain: V
Length: 112 nucleotides
Theoretical weight: 35.88 KDa
Sequence domains: U6 spliceosomal RNA

Ligands and Environments

3 bound ligands:
Ligand MG 2 x MG
Ligand ZN 7 x ZN
Ligand GTP 1 x GTP
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.8Å
Relevant EMDB volumes: EMD-4055

Quick links

Citations

36 review citations

Structural Insights into Nuclear pre-mRNA Splicing in Higher Eukaryotes.
Kastner et al. (2019)
35 more

20 mentions without citation

Structural Insights into the Mechanism of Group II Intron Splicing.
Zhao et al. (2017)
19 more