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Cryo-EM structure of the yeast B*-a1 complex at an average resolution of 3.6 angstrom

Electron Microscopy
3.6Å resolution
PDB entry 6j6h coloured by chain, front view.
PDB entry 6j6h coloured by chain, side view.
PDB entry 6j6h coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Assembly composition:
hetero 41-mer (preferred)
Entry contents: 27 distinct polypeptide molecules
4 distinct RNA molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero 41-mer
Accessible surface area: 465555.46 Å2
Buried surface area: 177930.32 Å2
Dissociation area: 187.29 Å2
Dissociation energy (ΔGdiss): -6.36 kcal/mol
Dissociation entropy (TΔSdiss): 7.37 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-149223

Macromolecules

Pre-mRNA-splicing factor 8
Chain: A
Length: 2413 amino acids
Theoretical weight: 279.87 KDa
Source organism: Saccharomyces cerevisiae S288C
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 6j6h, assembly 1, front view.
Pre-mRNA-splicing factor 8 in PDB entry 6j6h, assembly 1, side view.
Pre-mRNA-splicing factor 8 in PDB entry 6j6h, 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 S288C
UniProt:
  • Canonical: P36048 (Residues: 1-1008; Coverage: 100%)
Gene names: GIN10, SNU114, YKL173W, YKL637
Pfam:
InterPro:
Pre-mRNA-splicing factor SNU114 in PDB entry 6j6h, assembly 1, front view.
Pre-mRNA-splicing factor SNU114 in PDB entry 6j6h, assembly 1, side view.
Pre-mRNA-splicing factor SNU114 in PDB entry 6j6h, assembly 1, top view.
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Pre-mRNA-splicing factor CWC21
Chain: J
Length: 135 amino acids
Theoretical weight: 15.79 KDa
Source organism: Saccharomyces cerevisiae S288C
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 6j6h, assembly 1, front view.
Pre-mRNA-splicing factor CWC21 in PDB entry 6j6h, assembly 1, side view.
Pre-mRNA-splicing factor CWC21 in PDB entry 6j6h, assembly 1, top view.
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Pre-mRNA-splicing factor PRP46
Chain: O
Length: 451 amino acids
Theoretical weight: 50.77 KDa
Source organism: Saccharomyces cerevisiae S288C
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 6j6h, assembly 1, front view.
Pre-mRNA-splicing factor PRP46 in PDB entry 6j6h, assembly 1, side view.
Pre-mRNA-splicing factor PRP46 in PDB entry 6j6h, assembly 1, top view.
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Pre-mRNA-processing protein 45
Chain: P
Length: 379 amino acids
Theoretical weight: 42.55 KDa
Source organism: Saccharomyces cerevisiae S288C
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 6j6h, assembly 1, front view.
Pre-mRNA-processing protein 45 in PDB entry 6j6h, assembly 1, side view.
Pre-mRNA-processing protein 45 in PDB entry 6j6h, assembly 1, top view.
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Pre-mRNA-splicing factor SLT11
Chain: Q
Length: 364 amino acids
Theoretical weight: 40.99 KDa
Source organism: Saccharomyces cerevisiae S288C
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 6j6h, assembly 1, front view.
Pre-mRNA-splicing factor SLT11 in PDB entry 6j6h, assembly 1, side view.
Pre-mRNA-splicing factor SLT11 in PDB entry 6j6h, assembly 1, top view.
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Pre-mRNA-splicing factor CWC2
Chain: R
Length: 339 amino acids
Theoretical weight: 38.49 KDa
Source organism: Saccharomyces cerevisiae S288C
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 6j6h, assembly 1, front view.
Pre-mRNA-splicing factor CWC2 in PDB entry 6j6h, assembly 1, side view.
Pre-mRNA-splicing factor CWC2 in PDB entry 6j6h, assembly 1, top view.
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Pre-mRNA-splicing factor CWC15
Chain: S
Length: 175 amino acids
Theoretical weight: 19.98 KDa
Source organism: Saccharomyces cerevisiae S288C
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 6j6h, assembly 1, front view.
Pre-mRNA-splicing factor CWC15 in PDB entry 6j6h, assembly 1, side view.
Pre-mRNA-splicing factor CWC15 in PDB entry 6j6h, assembly 1, top view.
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Pre-mRNA-splicing factor BUD31
Chain: T
Length: 157 amino acids
Theoretical weight: 18.48 KDa
Source organism: Saccharomyces cerevisiae S288C
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 6j6h, assembly 1, front view.
Pre-mRNA-splicing factor BUD31 in PDB entry 6j6h, assembly 1, side view.
Pre-mRNA-splicing factor BUD31 in PDB entry 6j6h, assembly 1, top view.
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Pre-mRNA-splicing factor CWC22
Chain: Z
Length: 577 amino acids
Theoretical weight: 67.39 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P53333 (Residues: 1-577; Coverage: 100%)
Gene names: CWC22, YGR278W
Pfam: MA3 domain
InterPro:
Pre-mRNA-splicing factor CWC22 in PDB entry 6j6h, assembly 1, front view.
Pre-mRNA-splicing factor CWC22 in PDB entry 6j6h, assembly 1, side view.
Pre-mRNA-splicing factor CWC22 in PDB entry 6j6h, assembly 1, top view.
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Pre-mRNA-splicing factor CEF1
Chain: c
Length: 590 amino acids
Theoretical weight: 67.84 KDa
Source organism: Saccharomyces cerevisiae S288C
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 6j6h, assembly 1, front view.
Pre-mRNA-splicing factor CEF1 in PDB entry 6j6h, assembly 1, side view.
Pre-mRNA-splicing factor CEF1 in PDB entry 6j6h, assembly 1, top view.
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Pre-mRNA-splicing factor CLF1
Chain: d
Length: 687 amino acids
Theoretical weight: 82.56 KDa
Source organism: Saccharomyces cerevisiae S288C
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 6j6h, assembly 1, front view.
Pre-mRNA-splicing factor CLF1 in PDB entry 6j6h, assembly 1, side view.
Pre-mRNA-splicing factor CLF1 in PDB entry 6j6h, assembly 1, top view.
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Pre-mRNA-splicing factor SYF2
Chain: I
Length: 215 amino acids
Theoretical weight: 24.85 KDa
Source organism: Saccharomyces cerevisiae S288C
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 6j6h, assembly 1, front view.
Pre-mRNA-splicing factor SYF2 in PDB entry 6j6h, assembly 1, side view.
Pre-mRNA-splicing factor SYF2 in PDB entry 6j6h, assembly 1, top view.
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Pre-mRNA-processing factor 17
Chain: n
Length: 455 amino acids
Theoretical weight: 52.21 KDa
Source organism: Saccharomyces cerevisiae S288C
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 6j6h, assembly 1, front view.
Pre-mRNA-processing factor 17 in PDB entry 6j6h, assembly 1, side view.
Pre-mRNA-processing factor 17 in PDB entry 6j6h, assembly 1, top view.
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Pre-mRNA-splicing factor ISY1
Chain: H
Length: 235 amino acids
Theoretical weight: 28.07 KDa
Source organism: Saccharomyces cerevisiae S288C
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 6j6h, assembly 1, front view.
Pre-mRNA-splicing factor ISY1 in PDB entry 6j6h, assembly 1, side view.
Pre-mRNA-splicing factor ISY1 in PDB entry 6j6h, assembly 1, top view.
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Pre-mRNA-splicing factor SYF1
Chain: v
Length: 859 amino acids
Theoretical weight: 100.34 KDa
Source organism: Saccharomyces cerevisiae S288C
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 6j6h, assembly 1, front view.
Pre-mRNA-splicing factor SYF1 in PDB entry 6j6h, assembly 1, side view.
Pre-mRNA-splicing factor SYF1 in PDB entry 6j6h, assembly 1, top view.
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U2 small nuclear ribonucleoprotein B''
Chain: a
Length: 111 amino acids
Theoretical weight: 12.85 KDa
Source organism: Saccharomyces cerevisiae S288C
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 6j6h, assembly 1, front view.
U2 small nuclear ribonucleoprotein B'' in PDB entry 6j6h, assembly 1, side view.
U2 small nuclear ribonucleoprotein B'' in PDB entry 6j6h, assembly 1, top view.
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U2 small nuclear ribonucleoprotein A'
Chain: b
Length: 238 amino acids
Theoretical weight: 27.23 KDa
Source organism: Saccharomyces cerevisiae S288C
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 6j6h, assembly 1, front view.
U2 small nuclear ribonucleoprotein A' in PDB entry 6j6h, assembly 1, side view.
U2 small nuclear ribonucleoprotein A' in PDB entry 6j6h, assembly 1, top view.
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Pre-mRNA-splicing factor SNT309
Chain: t
Length: 175 amino acids
Theoretical weight: 20.74 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q06091 (Residues: 1-175; Coverage: 100%)
Gene names: NTC25, SNT309, YPR101W
Pre-mRNA-splicing factor SNT309 in PDB entry 6j6h, assembly 1, front view.
Pre-mRNA-splicing factor SNT309 in PDB entry 6j6h, assembly 1, side view.
Pre-mRNA-splicing factor SNT309 in PDB entry 6j6h, assembly 1, top view.
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Small nuclear ribonucleoprotein E
Chains: i, u
Length: 94 amino acids
Theoretical weight: 10.39 KDa
Source organism: Saccharomyces cerevisiae S288C
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 6j6h, assembly 1, front view.
Small nuclear ribonucleoprotein E in PDB entry 6j6h, assembly 1, side view.
Small nuclear ribonucleoprotein E in PDB entry 6j6h, assembly 1, top view.
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Small nuclear ribonucleoprotein Sm D1
Chains: m, z
Length: 146 amino acids
Theoretical weight: 16.3 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q02260 (Residues: 1-146; Coverage: 100%)
Gene names: SMD1, YGR074W
Pfam: LSM domain
InterPro:
Small nuclear ribonucleoprotein Sm D1 in PDB entry 6j6h, assembly 1, front view.
Small nuclear ribonucleoprotein Sm D1 in PDB entry 6j6h, assembly 1, side view.
Small nuclear ribonucleoprotein Sm D1 in PDB entry 6j6h, assembly 1, top view.
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Small nuclear ribonucleoprotein G
Chains: j, x
Length: 77 amino acids
Theoretical weight: 8.49 KDa
Source organism: Saccharomyces cerevisiae S288C
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 6j6h, assembly 1, front view.
Small nuclear ribonucleoprotein G in PDB entry 6j6h, assembly 1, side view.
Small nuclear ribonucleoprotein G in PDB entry 6j6h, assembly 1, top view.
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Small nuclear ribonucleoprotein F
Chains: h, w
Length: 86 amino acids
Theoretical weight: 9.67 KDa
Source organism: Saccharomyces cerevisiae S288C
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 6j6h, assembly 1, front view.
Small nuclear ribonucleoprotein F in PDB entry 6j6h, assembly 1, side view.
Small nuclear ribonucleoprotein F in PDB entry 6j6h, assembly 1, top view.
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Small nuclear ribonucleoprotein Sm D2
Chains: e, g
Length: 110 amino acids
Theoretical weight: 12.88 KDa
Source organism: Saccharomyces cerevisiae S288C
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 6j6h, assembly 1, front view.
Small nuclear ribonucleoprotein Sm D2 in PDB entry 6j6h, assembly 1, side view.
Small nuclear ribonucleoprotein Sm D2 in PDB entry 6j6h, assembly 1, top view.
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Small nuclear ribonucleoprotein-associated protein B
Chains: k, s
Length: 196 amino acids
Theoretical weight: 22.43 KDa
Source organism: Saccharomyces cerevisiae S288C
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 6j6h, assembly 1, front view.
Small nuclear ribonucleoprotein-associated protein B in PDB entry 6j6h, assembly 1, side view.
Small nuclear ribonucleoprotein-associated protein B in PDB entry 6j6h, assembly 1, top view.
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Small nuclear ribonucleoprotein Sm D3
Chains: l, y
Length: 101 amino acids
Theoretical weight: 11.24 KDa
Source organism: Saccharomyces cerevisiae S288C
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 6j6h, assembly 1, front view.
Small nuclear ribonucleoprotein Sm D3 in PDB entry 6j6h, assembly 1, side view.
Small nuclear ribonucleoprotein Sm D3 in PDB entry 6j6h, assembly 1, top view.
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Pre-mRNA-processing factor 19
Chains: o, p, q, r
Length: 503 amino acids
Theoretical weight: 56.63 KDa
Source organism: Saccharomyces cerevisiae S288C
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 6j6h, assembly 1, front view.
Pre-mRNA-processing factor 19 in PDB entry 6j6h, assembly 1, side view.
Pre-mRNA-processing factor 19 in PDB entry 6j6h, assembly 1, top view.
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RNA chain B
Name: ACT1 pre-mRNA
Representative chains: B
Length: 679 nucleotides
Theoretical weight: 217.1 KDa
ACT1 pre-mRNA in PDB entry 6j6h, assembly 1, front view.
ACT1 pre-mRNA in PDB entry 6j6h, assembly 1, side view.
ACT1 pre-mRNA in PDB entry 6j6h, assembly 1, top view.
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RNA chain D
Name: U5 snRNA
Representative chains: D
Length: 214 nucleotides
Theoretical weight: 68.64 KDa
Rfam: U5 spliceosomal RNA
U5 snRNA in PDB entry 6j6h, assembly 1, front view.
U5 snRNA in PDB entry 6j6h, assembly 1, side view.
U5 snRNA in PDB entry 6j6h, assembly 1, top view.
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RNA chain E
Name: U6 snRNA
Representative chains: E
Length: 112 nucleotides
Theoretical weight: 35.88 KDa
Rfam: U6 spliceosomal RNA
U6 snRNA in PDB entry 6j6h, assembly 1, front view.
U6 snRNA in PDB entry 6j6h, assembly 1, side view.
U6 snRNA in PDB entry 6j6h, assembly 1, top view.
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RNA chain L
Name: U2 snRNA
Representative chains: L
Length: 1175 nucleotides
Theoretical weight: 376.27 KDa
Rfam: U2 spliceosomal RNA
U2 snRNA in PDB entry 6j6h, assembly 1, front view.
U2 snRNA in PDB entry 6j6h, assembly 1, side view.
U2 snRNA in PDB entry 6j6h, assembly 1, top view.
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