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Structure of a spliceosome remodeled for exon ligation

Electron Microscopy
4.17Å resolution
PDB entry 5mq0 coloured by chain, front view.
PDB entry 5mq0 coloured by chain, side view.
PDB entry 5mq0 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Assembly composition:
hetero 46-mer (preferred)
Entry contents: 30 distinct polypeptide molecules
6 distinct RNA molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero 46-mer
Accessible surface area: 347767.41 Å2
Buried surface area: 159253.58 Å2
Dissociation area: 0 Å2
Dissociation energy (ΔGdiss): 0 kcal/mol
Dissociation entropy (TΔSdiss): 0 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-150217

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 5mq0, assembly 1, front view.
Pre-mRNA-splicing factor 8 in PDB entry 5mq0, assembly 1, side view.
Pre-mRNA-splicing factor 8 in PDB entry 5mq0, 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 5mq0, assembly 1, front view.
Pre-mRNA-splicing factor SNU114 in PDB entry 5mq0, assembly 1, side view.
Pre-mRNA-splicing factor SNU114 in PDB entry 5mq0, assembly 1, top view.
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Pre-mRNA-splicing factor CWC22
Chain: H
Length: 577 amino acids
Theoretical weight: 67.39 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P53333 (Residues: 1-577; Coverage: 100%)
Gene names: CWC22, YGR278W
Pfam: MA3 domain
InterPro:
Pre-mRNA-splicing factor CWC22 in PDB entry 5mq0, assembly 1, front view.
Pre-mRNA-splicing factor CWC22 in PDB entry 5mq0, assembly 1, side view.
Pre-mRNA-splicing factor CWC22 in PDB entry 5mq0, assembly 1, top view.
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Pre-mRNA-splicing factor PRP46
Chain: J
Length: 451 amino acids
Theoretical weight: 50.77 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:
Pre-mRNA-splicing factor PRP46 in PDB entry 5mq0, assembly 1, front view.
Pre-mRNA-splicing factor PRP46 in PDB entry 5mq0, assembly 1, side view.
Pre-mRNA-splicing factor PRP46 in PDB entry 5mq0, 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 5mq0, assembly 1, front view.
Pre-mRNA-processing protein 45 in PDB entry 5mq0, assembly 1, side view.
Pre-mRNA-processing protein 45 in PDB entry 5mq0, 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 5mq0, assembly 1, front view.
Pre-mRNA-splicing factor BUD31 in PDB entry 5mq0, assembly 1, side view.
Pre-mRNA-splicing factor BUD31 in PDB entry 5mq0, assembly 1, top view.
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Pre-mRNA-splicing factor CWC2
Chain: M
Length: 339 amino acids
Theoretical weight: 38.49 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 5mq0, assembly 1, front view.
Pre-mRNA-splicing factor CWC2 in PDB entry 5mq0, assembly 1, side view.
Pre-mRNA-splicing factor CWC2 in PDB entry 5mq0, 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 5mq0, assembly 1, front view.
Pre-mRNA-splicing factor SLT11 in PDB entry 5mq0, assembly 1, side view.
Pre-mRNA-splicing factor SLT11 in PDB entry 5mq0, assembly 1, top view.
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Pre-mRNA-splicing factor CEF1
Chain: O
Length: 590 amino acids
Theoretical weight: 67.84 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 5mq0, assembly 1, front view.
Pre-mRNA-splicing factor CEF1 in PDB entry 5mq0, assembly 1, side view.
Pre-mRNA-splicing factor CEF1 in PDB entry 5mq0, assembly 1, top view.
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Pre-mRNA-splicing factor CWC15
Chain: P
Length: 175 amino acids
Theoretical weight: 19.98 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 5mq0, assembly 1, front view.
Pre-mRNA-splicing factor CWC15 in PDB entry 5mq0, assembly 1, side view.
Pre-mRNA-splicing factor CWC15 in PDB entry 5mq0, 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 5mq0, assembly 1, front view.
Pre-mRNA-splicing factor CWC21 in PDB entry 5mq0, assembly 1, side view.
Pre-mRNA-splicing factor CWC21 in PDB entry 5mq0, assembly 1, top view.
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Pre-mRNA-splicing factor CLF1
Chain: S
Length: 687 amino acids
Theoretical weight: 82.56 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 5mq0, assembly 1, front view.
Pre-mRNA-splicing factor CLF1 in PDB entry 5mq0, assembly 1, side view.
Pre-mRNA-splicing factor CLF1 in PDB entry 5mq0, assembly 1, top view.
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Pre-mRNA-splicing factor SYF1
Chain: T
Length: 877 amino acids
Theoretical weight: 101.88 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 5mq0, assembly 1, front view.
Pre-mRNA-splicing factor SYF1 in PDB entry 5mq0, assembly 1, side view.
Pre-mRNA-splicing factor SYF1 in PDB entry 5mq0, assembly 1, top view.
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Pre-mRNA-splicing factor 18
Chain: a
Length: 251 amino acids
Theoretical weight: 28.41 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P33411 (Residues: 1-251; Coverage: 100%)
Gene names: PRP18, YGR006W
Pfam: Prp18 domain
InterPro:
Pre-mRNA-splicing factor 18 in PDB entry 5mq0, assembly 1, front view.
Pre-mRNA-splicing factor 18 in PDB entry 5mq0, assembly 1, side view.
Pre-mRNA-splicing factor 18 in PDB entry 5mq0, assembly 1, top view.
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Pre-mRNA-splicing factor SLU7
Chain: c
Length: 382 amino acids
Theoretical weight: 44.72 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q02775 (Residues: 1-382; Coverage: 100%)
Gene names: D4483, SLT17, SLU7, YDR088C
Pfam: Pre-mRNA splicing Prp18-interacting factor
InterPro:
Pre-mRNA-splicing factor SLU7 in PDB entry 5mq0, assembly 1, front view.
Pre-mRNA-splicing factor SLU7 in PDB entry 5mq0, assembly 1, side view.
Pre-mRNA-splicing factor SLU7 in PDB entry 5mq0, assembly 1, top view.
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Pre-mRNA-processing factor 17
Chain: o
Length: 455 amino acids
Theoretical weight: 52.13 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P40968 (Residues: 1-455; Coverage: 100%)
Gene names: CDC40, D9481.11, PRP17, SLU4, XRS2, YDR364C
Pfam: WD domain, G-beta repeat
InterPro:
Pre-mRNA-processing factor 17 in PDB entry 5mq0, assembly 1, front view.
Pre-mRNA-processing factor 17 in PDB entry 5mq0, assembly 1, side view.
Pre-mRNA-processing factor 17 in PDB entry 5mq0, assembly 1, top view.
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UNKNOWN PROTEIN
Chain: X
Length: 68 amino acids
Theoretical weight: 5.81 KDa
Source organism: Saccharomyces cerevisiae
UNKNOWN PROTEIN in PDB entry 5mq0, assembly 1, front view.
UNKNOWN PROTEIN in PDB entry 5mq0, assembly 1, side view.
UNKNOWN PROTEIN in PDB entry 5mq0, assembly 1, top view.
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Pre-mRNA-splicing factor SYF2
Chain: y
Length: 215 amino acids
Theoretical weight: 24.85 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P53277 (Residues: 1-215; Coverage: 100%)
Gene names: NTC31, SYF2, YGR129W
Pfam: SYF2 splicing factor
InterPro: mRNA splicing factor SYF2
Pre-mRNA-splicing factor SYF2 in PDB entry 5mq0, assembly 1, front view.
Pre-mRNA-splicing factor SYF2 in PDB entry 5mq0, assembly 1, side view.
Pre-mRNA-splicing factor SYF2 in PDB entry 5mq0, 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 5mq0, assembly 1, front view.
Small nuclear ribonucleoprotein-associated protein B in PDB entry 5mq0, assembly 1, side view.
Small nuclear ribonucleoprotein-associated protein B in PDB entry 5mq0, 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:
Small nuclear ribonucleoprotein Sm D3 in PDB entry 5mq0, assembly 1, front view.
Small nuclear ribonucleoprotein Sm D3 in PDB entry 5mq0, assembly 1, side view.
Small nuclear ribonucleoprotein Sm D3 in PDB entry 5mq0, 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:
Small nuclear ribonucleoprotein E in PDB entry 5mq0, assembly 1, front view.
Small nuclear ribonucleoprotein E in PDB entry 5mq0, assembly 1, side view.
Small nuclear ribonucleoprotein E in PDB entry 5mq0, 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:
Small nuclear ribonucleoprotein F in PDB entry 5mq0, assembly 1, front view.
Small nuclear ribonucleoprotein F in PDB entry 5mq0, assembly 1, side view.
Small nuclear ribonucleoprotein F in PDB entry 5mq0, 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:
Small nuclear ribonucleoprotein G in PDB entry 5mq0, assembly 1, front view.
Small nuclear ribonucleoprotein G in PDB entry 5mq0, assembly 1, side view.
Small nuclear ribonucleoprotein G in PDB entry 5mq0, 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:
Small nuclear ribonucleoprotein Sm D1 in PDB entry 5mq0, assembly 1, front view.
Small nuclear ribonucleoprotein Sm D1 in PDB entry 5mq0, assembly 1, side view.
Small nuclear ribonucleoprotein Sm D1 in PDB entry 5mq0, 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:
Small nuclear ribonucleoprotein Sm D2 in PDB entry 5mq0, assembly 1, front view.
Small nuclear ribonucleoprotein Sm D2 in PDB entry 5mq0, assembly 1, side view.
Small nuclear ribonucleoprotein Sm D2 in PDB entry 5mq0, assembly 1, top view.
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Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP22
Chain: V
Length: 1145 amino acids
Theoretical weight: 130.19 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P24384 (Residues: 1-1145; Coverage: 100%)
Gene names: PRP22, YER013W
Pfam:
InterPro:
Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP22 in PDB entry 5mq0, assembly 1, front view.
Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP22 in PDB entry 5mq0, assembly 1, side view.
Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP22 in PDB entry 5mq0, 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 5mq0, assembly 1, front view.
U2 small nuclear ribonucleoprotein A' in PDB entry 5mq0, assembly 1, side view.
U2 small nuclear ribonucleoprotein A' in PDB entry 5mq0, 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:
U2 small nuclear ribonucleoprotein B'' in PDB entry 5mq0, assembly 1, front view.
U2 small nuclear ribonucleoprotein B'' in PDB entry 5mq0, assembly 1, side view.
U2 small nuclear ribonucleoprotein B'' in PDB entry 5mq0, assembly 1, top view.
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Pre-mRNA-splicing factor SNT309
Chain: s
Length: 175 amino acids
Theoretical weight: 20.74 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q06091 (Residues: 1-175; Coverage: 100%)
Gene names: NTC25, SNT309, YPR101W
Pre-mRNA-splicing factor SNT309 in PDB entry 5mq0, assembly 1, front view.
Pre-mRNA-splicing factor SNT309 in PDB entry 5mq0, assembly 1, side view.
Pre-mRNA-splicing factor SNT309 in PDB entry 5mq0, assembly 1, top view.
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Pre-mRNA-processing factor 19
Chains: t, u, v, w
Length: 503 amino acids
Theoretical weight: 56.63 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P32523 (Residues: 1-503; Coverage: 100%)
Gene names: PRP19, PSO4, YLL036C
Pfam: Prp19/Pso4-like
InterPro:
Pre-mRNA-processing factor 19 in PDB entry 5mq0, assembly 1, front view.
Pre-mRNA-processing factor 19 in PDB entry 5mq0, assembly 1, side view.
Pre-mRNA-processing factor 19 in PDB entry 5mq0, assembly 1, top view.
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RNA chain I
Name: Yeast UBC4 gene for ubiquitin-conjugating enzyme
Representative chains: I
Length: 95 nucleotides
Theoretical weight: 30.2 KDa
Yeast UBC4 gene for ubiquitin-conjugating enzyme in PDB entry 5mq0, assembly 1, front view.
Yeast UBC4 gene for ubiquitin-conjugating enzyme in PDB entry 5mq0, assembly 1, side view.
Yeast UBC4 gene for ubiquitin-conjugating enzyme in PDB entry 5mq0, assembly 1, top view.
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RNA chain E
Name: 5'-EXON OF UBC4 PRE-MRNA
Representative chains: E
Length: 20 nucleotides
Theoretical weight: 6.52 KDa
5'-EXON OF UBC4 PRE-MRNA in PDB entry 5mq0, assembly 1, front view.
5'-EXON OF UBC4 PRE-MRNA in PDB entry 5mq0, assembly 1, side view.
5'-EXON OF UBC4 PRE-MRNA in PDB entry 5mq0, assembly 1, top view.
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RNA chain 2
Name: S.cerevisiae chromosome II reading frame ORF YBR230c
Representative chains: 2
Length: 1175 nucleotides
Theoretical weight: 376.27 KDa
Rfam: U2 spliceosomal RNA
S.cerevisiae chromosome II reading frame ORF YBR230c in PDB entry 5mq0, assembly 1, front view.
S.cerevisiae chromosome II reading frame ORF YBR230c in PDB entry 5mq0, assembly 1, side view.
S.cerevisiae chromosome II reading frame ORF YBR230c in PDB entry 5mq0, assembly 1, top view.
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RNA chain 6
Name: Saccharomyces cerevisiae strain T.52_2H chromosome XII sequence
Representative chains: 6
Length: 112 nucleotides
Theoretical weight: 35.88 KDa
Rfam: U6 spliceosomal RNA
Saccharomyces cerevisiae strain T.52_2H chromosome XII sequence in PDB entry 5mq0, assembly 1, front view.
Saccharomyces cerevisiae strain T.52_2H chromosome XII sequence in PDB entry 5mq0, assembly 1, side view.
Saccharomyces cerevisiae strain T.52_2H chromosome XII sequence in PDB entry 5mq0, assembly 1, top view.
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RNA chain 5
Name: Saccharomyces cerevisiae strain WI_C_MBSP_4 chromosome VII sequence
Representative chains: 5
Length: 179 nucleotides
Theoretical weight: 57.44 KDa
Rfam: U5 spliceosomal RNA
Saccharomyces cerevisiae strain WI_C_MBSP_4 chromosome VII sequence in PDB entry 5mq0, assembly 1, front view.
Saccharomyces cerevisiae strain WI_C_MBSP_4 chromosome VII sequence in PDB entry 5mq0, assembly 1, side view.
Saccharomyces cerevisiae strain WI_C_MBSP_4 chromosome VII sequence in PDB entry 5mq0, assembly 1, top view.
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RNA chain 3
Name: 3'-EXON OF UBC4 PRE-MRNA, BOUND BY PRP22 HELICASE
Representative chains: 3
Length: 3 nucleotides
Theoretical weight: 874 Da
3'-EXON OF UBC4 PRE-MRNA, BOUND BY PRP22 HELICASE in PDB entry 5mq0, assembly 1, front view.
3'-EXON OF UBC4 PRE-MRNA, BOUND BY PRP22 HELICASE in PDB entry 5mq0, assembly 1, side view.
3'-EXON OF UBC4 PRE-MRNA, BOUND BY PRP22 HELICASE in PDB entry 5mq0, assembly 1, top view.
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