5lj3

Electron Microscopy
3.8Å resolution

Structure of the core of the yeast spliceosome immediately after branching

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero 38-mer (preferred)
Entry contents:
26 distinct polypeptide molecules
5 distinct RNA molecules
Macromolecules (31 distinct):
Pre-mRNA-splicing factor 8 Chain: A
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: G10 protein
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
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:
No modified residues

Experiments and Validation Details

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