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yeast activated spliceosome

Electron Microscopy
5.8Å resolution
PDB entry 5lqw coloured by chain, front view.
PDB entry 5lqw coloured by chain, side view.
PDB entry 5lqw coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Assembly composition:
hetero 31-mer (preferred)
Entry contents: 27 distinct polypeptide molecules
4 distinct RNA molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Sm complex and RNA
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Multimeric state: hetero 31-mer
Accessible surface area: 80992.9 Å2
Buried surface area: 5134.44 Å2
Dissociation area: 374.18 Å2
Dissociation energy (ΔGdiss): 2.27 kcal/mol
Dissociation entropy (TΔSdiss): 15.22 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-142865

Macromolecules

Pre-mRNA-splicing factor 8
Chain: A
Length: 2413 amino acids
Theoretical weight: 279.85 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 5lqw, assembly 1, front view.
Pre-mRNA-splicing factor 8 in PDB entry 5lqw, assembly 1, side view.
Pre-mRNA-splicing factor 8 in PDB entry 5lqw, assembly 1, top view.
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Pre-mRNA-splicing factor SNU114
Chain: B
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 5lqw, assembly 1, front view.
Pre-mRNA-splicing factor SNU114 in PDB entry 5lqw, assembly 1, side view.
Pre-mRNA-splicing factor SNU114 in PDB entry 5lqw, assembly 1, top view.
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Pre-mRNA-splicing helicase BRR2
Chain: C
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
Pfam:
InterPro:
Pre-mRNA-splicing helicase BRR2 in PDB entry 5lqw, assembly 1, front view.
Pre-mRNA-splicing helicase BRR2 in PDB entry 5lqw, assembly 1, side view.
Pre-mRNA-splicing helicase BRR2 in PDB entry 5lqw, assembly 1, top view.
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Pre-mRNA-splicing factor SLT11
Chain: D
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 5lqw, assembly 1, front view.
Pre-mRNA-splicing factor SLT11 in PDB entry 5lqw, assembly 1, side view.
Pre-mRNA-splicing factor SLT11 in PDB entry 5lqw, assembly 1, top view.
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Pre-mRNA-splicing factor BUD31
Chain: E
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 5lqw, assembly 1, front view.
Pre-mRNA-splicing factor BUD31 in PDB entry 5lqw, assembly 1, side view.
Pre-mRNA-splicing factor BUD31 in PDB entry 5lqw, assembly 1, top view.
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Pre-mRNA-splicing factor CWC2
Chain: F
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 5lqw, assembly 1, front view.
Pre-mRNA-splicing factor CWC2 in PDB entry 5lqw, assembly 1, side view.
Pre-mRNA-splicing factor CWC2 in PDB entry 5lqw, 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 5lqw, assembly 1, front view.
Pre-mRNA-splicing factor CWC22 in PDB entry 5lqw, assembly 1, side view.
Pre-mRNA-splicing factor CWC22 in PDB entry 5lqw, assembly 1, top view.
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U2 snRNP component IST3
Chain: J
Length: 148 amino acids
Theoretical weight: 17.12 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P40565 (Residues: 1-148; Coverage: 100%)
Gene names: IST3, SNU17, YIB5W, YIR005W
Pfam: RNA recognition motif
InterPro:
U2 snRNP component IST3 in PDB entry 5lqw, assembly 1, front view.
U2 snRNP component IST3 in PDB entry 5lqw, assembly 1, side view.
U2 snRNP component IST3 in PDB entry 5lqw, assembly 1, top view.
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Pre-mRNA-splicing factor PRP46
Chain: K
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 5lqw, assembly 1, front view.
Pre-mRNA-splicing factor PRP46 in PDB entry 5lqw, assembly 1, side view.
Pre-mRNA-splicing factor PRP46 in PDB entry 5lqw, assembly 1, top view.
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Pre-mRNA-splicing factor CWC26
Chain: L
Length: 266 amino acids
Theoretical weight: 30.53 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P46947 (Residues: 1-266; Coverage: 100%)
Gene names: BUD13, CWC26, G1642, SLC7, YGL174W
Pfam: Pre-mRNA-splicing factor of RES complex
InterPro: Bud13
Pre-mRNA-splicing factor CWC26 in PDB entry 5lqw, assembly 1, front view.
Pre-mRNA-splicing factor CWC26 in PDB entry 5lqw, assembly 1, side view.
Pre-mRNA-splicing factor CWC26 in PDB entry 5lqw, assembly 1, top view.
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Pre-mRNA-processing protein 45
Chain: M
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 5lqw, assembly 1, front view.
Pre-mRNA-processing protein 45 in PDB entry 5lqw, assembly 1, side view.
Pre-mRNA-processing protein 45 in PDB entry 5lqw, assembly 1, top view.
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Pre-mRNA leakage protein 1
Chain: N
Length: 204 amino acids
Theoretical weight: 23.69 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q07930 (Residues: 1-204; Coverage: 100%)
Gene names: L1591, PML1, YLR016C
Pfam: FHA domain
InterPro:
Pre-mRNA leakage protein 1 in PDB entry 5lqw, assembly 1, front view.
Pre-mRNA leakage protein 1 in PDB entry 5lqw, assembly 1, side view.
Pre-mRNA leakage protein 1 in PDB entry 5lqw, assembly 1, top view.
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Pre-mRNA-splicing factor ATP-dependent RNA helicase-like protein PRP2
Chain: O
Length: 876 amino acids
Theoretical weight: 99.95 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P20095 (Residues: 1-876; Coverage: 100%)
Gene names: N2048, PRP2, RNA2, YNR011C
Pfam:
InterPro:
Pre-mRNA-splicing factor ATP-dependent RNA helicase-like protein PRP2 in PDB entry 5lqw, assembly 1, front view.
Pre-mRNA-splicing factor ATP-dependent RNA helicase-like protein PRP2 in PDB entry 5lqw, assembly 1, side view.
Pre-mRNA-splicing factor ATP-dependent RNA helicase-like protein PRP2 in PDB entry 5lqw, assembly 1, top view.
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Pre-mRNA-splicing factor SYF1
Chain: P
Length: 859 amino acids
Theoretical weight: 100.34 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q04048 (Residues: 1-859; Coverage: 100%)
Gene names: NTC90, SYF1, YDR416W
InterPro:
Pre-mRNA-splicing factor SYF1 in PDB entry 5lqw, assembly 1, front view.
Pre-mRNA-splicing factor SYF1 in PDB entry 5lqw, assembly 1, side view.
Pre-mRNA-splicing factor SYF1 in PDB entry 5lqw, assembly 1, top view.
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U2 snRNP component HSH155
Chain: Q
Length: 971 amino acids
Theoretical weight: 110.17 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P49955 (Residues: 1-971; Coverage: 100%)
Gene names: HSH155, YM8021.14, YMR288W
InterPro:
U2 snRNP component HSH155 in PDB entry 5lqw, assembly 1, front view.
U2 snRNP component HSH155 in PDB entry 5lqw, assembly 1, side view.
U2 snRNP component HSH155 in PDB entry 5lqw, assembly 1, top view.
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Pre-mRNA-splicing factor CLF1
Chain: R
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: HAT (Half-A-TPR) repeat
InterPro:
Pre-mRNA-splicing factor CLF1 in PDB entry 5lqw, assembly 1, front view.
Pre-mRNA-splicing factor CLF1 in PDB entry 5lqw, assembly 1, side view.
Pre-mRNA-splicing factor CLF1 in PDB entry 5lqw, assembly 1, top view.
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Pre-mRNA-splicing factor CEF1
Chain: W
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 5lqw, assembly 1, front view.
Pre-mRNA-splicing factor CEF1 in PDB entry 5lqw, assembly 1, side view.
Pre-mRNA-splicing factor CEF1 in PDB entry 5lqw, assembly 1, top view.
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Pre-mRNA-splicing factor RSE1
Chain: X
Length: 1361 amino acids
Theoretical weight: 153.96 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q04693 (Residues: 1-1361; Coverage: 100%)
Gene names: RSE1, SAP130, YM9827.03C, YML049C
Pfam:
InterPro:
Pre-mRNA-splicing factor RSE1 in PDB entry 5lqw, assembly 1, front view.
Pre-mRNA-splicing factor RSE1 in PDB entry 5lqw, assembly 1, side view.
Pre-mRNA-splicing factor RSE1 in PDB entry 5lqw, assembly 1, top view.
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Pre-mRNA-splicing factor RDS3
Chain: Y
Length: 107 amino acids
Theoretical weight: 12.28 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q06835 (Residues: 1-107; Coverage: 100%)
Gene names: P9513.2, RDS3, YPR094W
Pfam: PHF5-like protein
InterPro: PHF5-like
Pre-mRNA-splicing factor RDS3 in PDB entry 5lqw, assembly 1, front view.
Pre-mRNA-splicing factor RDS3 in PDB entry 5lqw, assembly 1, side view.
Pre-mRNA-splicing factor RDS3 in PDB entry 5lqw, assembly 1, top view.
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RDS3 complex subunit 10
Chain: Z
Length: 85 amino acids
Theoretical weight: 10.05 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0C074 (Residues: 1-85; Coverage: 100%)
Gene names: RCP10, YNL138W-A, YSF3
Pfam: Splicing factor 3B subunit 10 (SF3b10)
InterPro: Splicing factor 3B subunit 5/RDS3 complex subunit 10
RDS3 complex subunit 10 in PDB entry 5lqw, assembly 1, front view.
RDS3 complex subunit 10 in PDB entry 5lqw, assembly 1, side view.
RDS3 complex subunit 10 in PDB entry 5lqw, assembly 1, top view.
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Small nuclear ribonucleoprotein-associated protein B
Chain: b
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 5lqw, assembly 1, front view.
Small nuclear ribonucleoprotein-associated protein B in PDB entry 5lqw, assembly 1, side view.
Small nuclear ribonucleoprotein-associated protein B in PDB entry 5lqw, assembly 1, top view.
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Small nuclear ribonucleoprotein Sm D3
Chain: d
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 5lqw, assembly 1, front view.
Small nuclear ribonucleoprotein Sm D3 in PDB entry 5lqw, assembly 1, side view.
Small nuclear ribonucleoprotein Sm D3 in PDB entry 5lqw, assembly 1, top view.
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Small nuclear ribonucleoprotein E
Chain: e
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 5lqw, assembly 1, front view.
Small nuclear ribonucleoprotein E in PDB entry 5lqw, assembly 1, side view.
Small nuclear ribonucleoprotein E in PDB entry 5lqw, assembly 1, top view.
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Small nuclear ribonucleoprotein F
Chain: f
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 5lqw, assembly 1, front view.
Small nuclear ribonucleoprotein F in PDB entry 5lqw, assembly 1, side view.
Small nuclear ribonucleoprotein F in PDB entry 5lqw, assembly 1, top view.
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Small nuclear ribonucleoprotein G
Chain: g
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 5lqw, assembly 1, front view.
Small nuclear ribonucleoprotein G in PDB entry 5lqw, assembly 1, side view.
Small nuclear ribonucleoprotein G in PDB entry 5lqw, assembly 1, top view.
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Small nuclear ribonucleoprotein Sm D1
Chain: h
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 5lqw, assembly 1, front view.
Small nuclear ribonucleoprotein Sm D1 in PDB entry 5lqw, assembly 1, side view.
Small nuclear ribonucleoprotein Sm D1 in PDB entry 5lqw, assembly 1, top view.
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Small nuclear ribonucleoprotein Sm D2
Chain: j
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 5lqw, assembly 1, front view.
Small nuclear ribonucleoprotein Sm D2 in PDB entry 5lqw, assembly 1, side view.
Small nuclear ribonucleoprotein Sm D2 in PDB entry 5lqw, assembly 1, top view.
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RNA chain 2
Name: U2 snRNA
Representative chains: 2
Length: 1175 nucleotides
Theoretical weight: 376.27 KDa
Rfam: U2 spliceosomal RNA
U2 snRNA in PDB entry 5lqw, assembly 1, front view.
U2 snRNA in PDB entry 5lqw, assembly 1, side view.
U2 snRNA in PDB entry 5lqw, assembly 1, top view.
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RNA chain 5
Name: U5 snRNA
Representative chains: 5
Length: 179 nucleotides
Theoretical weight: 57.44 KDa
Rfam: U5 spliceosomal RNA
U5 snRNA in PDB entry 5lqw, assembly 1, front view.
U5 snRNA in PDB entry 5lqw, assembly 1, side view.
U5 snRNA in PDB entry 5lqw, assembly 1, top view.
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RNA chain 6
Name: U6 snRNA
Representative chains: 6
Length: 112 nucleotides
Theoretical weight: 35.88 KDa
Rfam: U6 spliceosomal RNA
U6 snRNA in PDB entry 5lqw, assembly 1, front view.
U6 snRNA in PDB entry 5lqw, assembly 1, side view.
U6 snRNA in PDB entry 5lqw, assembly 1, top view.
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RNA chain 9
Name: actin pre-mRNA
Representative chains: 9
Length: 572 nucleotides
Theoretical weight: 182.57 KDa
actin pre-mRNA in PDB entry 5lqw, assembly 1, front view.
actin pre-mRNA in PDB entry 5lqw, assembly 1, side view.
actin pre-mRNA in PDB entry 5lqw, assembly 1, top view.
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