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Structure of the core of the yeast spliceosome immediately after branching

Electron Microscopy
3.8Å resolution
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
Assembly composition:
hetero 38-mer (preferred)
Entry contents: 26 distinct polypeptide molecules
5 distinct RNA molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero 38-mer
Accessible surface area: 317162.23 Å2
Buried surface area: 137368.0 Å2
Dissociation area: 2,011.37 Å2
Dissociation energy (ΔGdiss): 18.65 kcal/mol
Dissociation entropy (TΔSdiss): 13.23 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-149221

Macromolecules

Pre-mRNA-splicing factor 8
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
Pfam:
InterPro:
Pre-mRNA-splicing factor 8 in PDB entry 5lj3, assembly 1, front view.
Pre-mRNA-splicing factor 8 in PDB entry 5lj3, assembly 1, side view.
Pre-mRNA-splicing factor 8 in PDB entry 5lj3, assembly 1, top view.
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Splicing factor YJU2
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
Pfam: Saf4/Yju2 protein
InterPro:
Splicing factor YJU2 in PDB entry 5lj3, assembly 1, front view.
Splicing factor YJU2 in PDB entry 5lj3, assembly 1, side view.
Splicing factor YJU2 in PDB entry 5lj3, assembly 1, top view.
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Pre-mRNA-splicing factor CWC25
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
Pfam:
InterPro:
Pre-mRNA-splicing factor CWC25 in PDB entry 5lj3, assembly 1, front view.
Pre-mRNA-splicing factor CWC25 in PDB entry 5lj3, assembly 1, side view.
Pre-mRNA-splicing factor CWC25 in PDB entry 5lj3, assembly 1, top view.
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Pre-mRNA-splicing factor SNU114
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
Pfam:
InterPro:
Pre-mRNA-splicing factor SNU114 in PDB entry 5lj3, assembly 1, front view.
Pre-mRNA-splicing factor SNU114 in PDB entry 5lj3, assembly 1, side view.
Pre-mRNA-splicing factor SNU114 in PDB entry 5lj3, assembly 1, top view.
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Pre-mRNA-splicing factor ISY1
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
Pfam: Isy1-like splicing family
InterPro:
Pre-mRNA-splicing factor ISY1 in PDB entry 5lj3, assembly 1, front view.
Pre-mRNA-splicing factor ISY1 in PDB entry 5lj3, assembly 1, side view.
Pre-mRNA-splicing factor ISY1 in PDB entry 5lj3, assembly 1, top view.
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CWC22
Chain: H
Length: 591 amino acids
Theoretical weight: 69.12 KDa
Source organism: Saccharomyces cerevisiae
InterPro:
CWC22 in PDB entry 5lj3, assembly 1, front view.
CWC22 in PDB entry 5lj3, assembly 1, side view.
CWC22 in PDB entry 5lj3, assembly 1, top view.
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Pre-mRNA-splicing factor PRP46
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
Pfam: WD domain, G-beta repeat
InterPro:
CATH: YVTN repeat-like/Quinoprotein amine dehydrogenase
Pre-mRNA-splicing factor PRP46 in PDB entry 5lj3, assembly 1, front view.
Pre-mRNA-splicing factor PRP46 in PDB entry 5lj3, assembly 1, side view.
Pre-mRNA-splicing factor PRP46 in PDB entry 5lj3, assembly 1, top view.
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Pre-mRNA-processing protein 45
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
Pfam: SKIP/SNW domain
InterPro:
Pre-mRNA-processing protein 45 in PDB entry 5lj3, assembly 1, front view.
Pre-mRNA-processing protein 45 in PDB entry 5lj3, assembly 1, side view.
Pre-mRNA-processing protein 45 in PDB entry 5lj3, assembly 1, top view.
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Pre-mRNA-splicing factor BUD31
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
Pfam: Pre-mRNA-splicing factor BUD31
InterPro:
Pre-mRNA-splicing factor BUD31 in PDB entry 5lj3, assembly 1, front view.
Pre-mRNA-splicing factor BUD31 in PDB entry 5lj3, assembly 1, side view.
Pre-mRNA-splicing factor BUD31 in PDB entry 5lj3, assembly 1, top view.
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Pre-mRNA-splicing factor CWC2
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
Pfam:
InterPro:
Pre-mRNA-splicing factor CWC2 in PDB entry 5lj3, assembly 1, front view.
Pre-mRNA-splicing factor CWC2 in PDB entry 5lj3, assembly 1, side view.
Pre-mRNA-splicing factor CWC2 in PDB entry 5lj3, assembly 1, top view.
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Pre-mRNA-splicing factor SLT11
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
Pfam: STL11, N-terminal
InterPro:
Pre-mRNA-splicing factor SLT11 in PDB entry 5lj3, assembly 1, front view.
Pre-mRNA-splicing factor SLT11 in PDB entry 5lj3, assembly 1, side view.
Pre-mRNA-splicing factor SLT11 in PDB entry 5lj3, assembly 1, top view.
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Pre-mRNA-splicing factor CEF1
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
Pfam:
InterPro:
Pre-mRNA-splicing factor CEF1 in PDB entry 5lj3, assembly 1, front view.
Pre-mRNA-splicing factor CEF1 in PDB entry 5lj3, assembly 1, side view.
Pre-mRNA-splicing factor CEF1 in PDB entry 5lj3, assembly 1, top view.
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Pre-mRNA-splicing factor CWC15
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
Pfam: Cwf15/Cwc15 cell cycle control protein
InterPro: Pre-mRNA-splicing factor Cwf15/Cwc15
Pre-mRNA-splicing factor CWC15 in PDB entry 5lj3, assembly 1, front view.
Pre-mRNA-splicing factor CWC15 in PDB entry 5lj3, assembly 1, side view.
Pre-mRNA-splicing factor CWC15 in PDB entry 5lj3, assembly 1, top view.
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Pre-mRNA-splicing factor CWC21
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
Pfam: cwf21 domain
InterPro: mRNA splicing factor Cwf21 domain
Pre-mRNA-splicing factor CWC21 in PDB entry 5lj3, assembly 1, front view.
Pre-mRNA-splicing factor CWC21 in PDB entry 5lj3, assembly 1, side view.
Pre-mRNA-splicing factor CWC21 in PDB entry 5lj3, assembly 1, top view.
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Pre-mRNA-splicing factor CLF1
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
Pfam: Suppressor of forked protein (Suf)
InterPro:
Pre-mRNA-splicing factor CLF1 in PDB entry 5lj3, assembly 1, front view.
Pre-mRNA-splicing factor CLF1 in PDB entry 5lj3, assembly 1, side view.
Pre-mRNA-splicing factor CLF1 in PDB entry 5lj3, assembly 1, top view.
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Pre-mRNA-splicing factor SYF1
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
Pfam: Suppressor of forked protein (Suf)
InterPro:
Pre-mRNA-splicing factor SYF1 in PDB entry 5lj3, assembly 1, front view.
Pre-mRNA-splicing factor SYF1 in PDB entry 5lj3, assembly 1, side view.
Pre-mRNA-splicing factor SYF1 in PDB entry 5lj3, assembly 1, top view.
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Small nuclear ribonucleoprotein-associated protein B
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
Pfam: LSM domain
InterPro:
Small nuclear ribonucleoprotein-associated protein B in PDB entry 5lj3, assembly 1, front view.
Small nuclear ribonucleoprotein-associated protein B in PDB entry 5lj3, assembly 1, side view.
Small nuclear ribonucleoprotein-associated protein B in PDB entry 5lj3, assembly 1, top view.
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Small nuclear ribonucleoprotein Sm D3
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
Pfam: LSM domain
InterPro:
CATH: SH3 type barrels.
Small nuclear ribonucleoprotein Sm D3 in PDB entry 5lj3, assembly 1, front view.
Small nuclear ribonucleoprotein Sm D3 in PDB entry 5lj3, assembly 1, side view.
Small nuclear ribonucleoprotein Sm D3 in PDB entry 5lj3, assembly 1, top view.
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Small nuclear ribonucleoprotein E
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
Pfam: LSM domain
InterPro:
CATH: SH3 type barrels.
Small nuclear ribonucleoprotein E in PDB entry 5lj3, assembly 1, front view.
Small nuclear ribonucleoprotein E in PDB entry 5lj3, assembly 1, side view.
Small nuclear ribonucleoprotein E in PDB entry 5lj3, assembly 1, top view.
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Small nuclear ribonucleoprotein F
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
Pfam: LSM domain
InterPro:
CATH: SH3 type barrels.
Small nuclear ribonucleoprotein F in PDB entry 5lj3, assembly 1, front view.
Small nuclear ribonucleoprotein F in PDB entry 5lj3, assembly 1, side view.
Small nuclear ribonucleoprotein F in PDB entry 5lj3, assembly 1, top view.
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Small nuclear ribonucleoprotein G
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
Pfam: LSM domain
InterPro:
CATH: SH3 type barrels.
Small nuclear ribonucleoprotein G in PDB entry 5lj3, assembly 1, front view.
Small nuclear ribonucleoprotein G in PDB entry 5lj3, assembly 1, side view.
Small nuclear ribonucleoprotein G in PDB entry 5lj3, assembly 1, top view.
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Small nuclear ribonucleoprotein Sm D1
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
Pfam: LSM domain
InterPro:
CATH: SH3 type barrels.
Small nuclear ribonucleoprotein Sm D1 in PDB entry 5lj3, assembly 1, front view.
Small nuclear ribonucleoprotein Sm D1 in PDB entry 5lj3, assembly 1, side view.
Small nuclear ribonucleoprotein Sm D1 in PDB entry 5lj3, assembly 1, top view.
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Small nuclear ribonucleoprotein Sm D2
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
Pfam: LSM domain
InterPro:
CATH: SH3 type barrels.
Small nuclear ribonucleoprotein Sm D2 in PDB entry 5lj3, assembly 1, front view.
Small nuclear ribonucleoprotein Sm D2 in PDB entry 5lj3, assembly 1, side view.
Small nuclear ribonucleoprotein Sm D2 in PDB entry 5lj3, assembly 1, top view.
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U2 small nuclear ribonucleoprotein A'
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
Pfam: Leucine-rich repeat
InterPro:
U2 small nuclear ribonucleoprotein A' in PDB entry 5lj3, assembly 1, front view.
U2 small nuclear ribonucleoprotein A' in PDB entry 5lj3, assembly 1, side view.
U2 small nuclear ribonucleoprotein A' in PDB entry 5lj3, assembly 1, top view.
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U2 small nuclear ribonucleoprotein B''
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
Pfam: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
InterPro:
CATH: Alpha-Beta Plaits
U2 small nuclear ribonucleoprotein B'' in PDB entry 5lj3, assembly 1, front view.
U2 small nuclear ribonucleoprotein B'' in PDB entry 5lj3, assembly 1, side view.
U2 small nuclear ribonucleoprotein B'' in PDB entry 5lj3, assembly 1, top view.
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unknown
Chain: x
Length: 132 amino acids
Theoretical weight: 11.25 KDa
Source organism: Saccharomyces cerevisiae
unknown in PDB entry 5lj3, assembly 1, front view.
unknown in PDB entry 5lj3, assembly 1, side view.
unknown in PDB entry 5lj3, assembly 1, top view.
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RNA chain U
Name: U5 snRNA (small nuclear RNA)
Representative chains: U
Length: 179 nucleotides
Theoretical weight: 57.44 KDa
Rfam: U5 spliceosomal RNA
U5 snRNA (small nuclear RNA) in PDB entry 5lj3, assembly 1, front view.
U5 snRNA (small nuclear RNA) in PDB entry 5lj3, assembly 1, side view.
U5 snRNA (small nuclear RNA) in PDB entry 5lj3, assembly 1, top view.
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RNA chain E
Name: Exon 1 (5' exon) of UBC4 pre-mRNA
Representative chains: E
Length: 16 nucleotides
Theoretical weight: 5.17 KDa
Exon 1 (5' exon) of UBC4 pre-mRNA in PDB entry 5lj3, assembly 1, front view.
Exon 1 (5' exon) of UBC4 pre-mRNA in PDB entry 5lj3, assembly 1, side view.
Exon 1 (5' exon) of UBC4 pre-mRNA in PDB entry 5lj3, assembly 1, top view.
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RNA chain I
Name: Intron of UBC4 pre-mRNA
Representative chains: I
Length: 76 nucleotides
Theoretical weight: 24.11 KDa
Intron of UBC4 pre-mRNA in PDB entry 5lj3, assembly 1, front view.
Intron of UBC4 pre-mRNA in PDB entry 5lj3, assembly 1, side view.
Intron of UBC4 pre-mRNA in PDB entry 5lj3, assembly 1, top view.
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RNA chain Z
Name: U2 snRNA (small nuclear RNA)
Representative chains: Z
Length: 1175 nucleotides
Theoretical weight: 376.27 KDa
Rfam: U2 spliceosomal RNA
U2 snRNA (small nuclear RNA) in PDB entry 5lj3, assembly 1, front view.
U2 snRNA (small nuclear RNA) in PDB entry 5lj3, assembly 1, side view.
U2 snRNA (small nuclear RNA) in PDB entry 5lj3, assembly 1, top view.
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RNA chain V
Name: U6 snRNA (small nuclear RNA)
Representative chains: V
Length: 112 nucleotides
Theoretical weight: 35.88 KDa
Rfam: U6 spliceosomal RNA
U6 snRNA (small nuclear RNA) in PDB entry 5lj3, assembly 1, front view.
U6 snRNA (small nuclear RNA) in PDB entry 5lj3, assembly 1, side view.
U6 snRNA (small nuclear RNA) in PDB entry 5lj3, assembly 1, top view.
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