› 6g90

Electron Microscopy
4Å resolution

Prespliceosome structure provides insight into spliceosome assembly and regulation (map A2)

Released:
DOI: 10.2210/pdb6g90/pdb
PDB entry 6g90 coloured by chain, front view.
PDB entry 6g90 coloured by chain, side view.
PDB entry 6g90 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Prespliceosome structure provides insights into spliceosome assembly and regulation.
Plaschka C, Lin PC, Charenton C, Nagai K
Nature 559 419-422 (2018)
PMID: 29995849
Related structures: EMD-4364

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 38-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-142863 (preferred)
Entry contents:
28 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (31 distinct):
U1 small nuclear ribonucleoprotein A Chain: A
Molecule details ›
Chain: A
Length: 298 amino acids
Theoretical weight: 33.75 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P32605 (Residues: 1-298; Coverage: 100%)
Gene names: MUD1, YBR0915, YBR119W
Sequence domains: RNA recognition motif
U1 small nuclear ribonucleoprotein 70 kDa homolog Chain: B
Molecule details ›
Chain: B
Length: 300 amino acids
Theoretical weight: 33.45 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q00916 (Residues: 1-300; Coverage: 100%)
Gene names: SNP1, YIL061C
Sequence domains:
U1 small nuclear ribonucleoprotein C Chain: C
Molecule details ›
Chain: C
Length: 231 amino acids
Theoretical weight: 27.11 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q05900 (Residues: 1-231; Coverage: 100%)
Gene names: L8003.21, YHC1, YLR298C
Sequence domains: U1 zinc finger
Pre-mRNA-processing factor 39 Chain: D
Molecule details ›
Chain: D
Length: 629 amino acids
Theoretical weight: 74.83 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P39682 (Residues: 1-629; Coverage: 100%)
Gene names: PRP39, YM9827.06, YML046W
U1 small nuclear ribonucleoprotein component PRP42 Chain: E
Molecule details ›
Chain: E
Length: 544 amino acids
Theoretical weight: 65.22 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q03776 (Residues: 1-544; Coverage: 100%)
Gene names: MUD16, PRP42, SNU65, YD8419.02, YDR235W
Protein NAM8 Chain: F
Molecule details ›
Chain: F
Length: 523 amino acids
Theoretical weight: 57.01 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q00539 (Residues: 1-523; Coverage: 100%)
Gene names: MRE2, MUD15, NAM8, YHR086W
Sequence domains: RNA recognition motif
56 kDa U1 small nuclear ribonucleoprotein component Chain: G
Molecule details ›
Chain: G
Length: 492 amino acids
Theoretical weight: 56.58 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q03782 (Residues: 1-492; Coverage: 100%)
Gene names: MUD10, SNU56, YDR240C
Sequence domains: Snu56-like U1 small nuclear ribonucleoprotein component
Protein LUC7 Chain: H
Molecule details ›
Chain: H
Length: 261 amino acids
Theoretical weight: 28.5 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q07508 (Residues: 1-261; Coverage: 100%)
Gene names: EPE1, EXM2, LUC7, YDL087C
Sequence domains: LUC7 N_terminus
U1 small nuclear ribonucleoprotein component SNU71 Chain: J
Molecule details ›
Chain: J
Length: 620 amino acids
Theoretical weight: 71.48 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P53207 (Residues: 1-620; Coverage: 100%)
Gene names: SNU71, YGR013W
U2 snRNP component HSH155 Chain: O
Molecule details ›
Chain: O
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
Pre-mRNA-splicing factor RSE1 Chain: P
Molecule details ›
Chain: P
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
Sequence domains:
Cold sensitive U2 snRNA suppressor 1 Chain: Q
Molecule details ›
Chain: Q
Length: 435 amino acids
Theoretical weight: 50.21 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q02554 (Residues: 1-435; Coverage: 100%)
Gene names: CUS1, YM9408.02C, YMR240C
Sequence domains:
Protein HSH49 Chain: R
Molecule details ›
Chain: R
Length: 213 amino acids
Theoretical weight: 24.53 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q99181 (Residues: 1-213; Coverage: 100%)
Gene names: HSH49, O6142, YOR319W
Sequence domains: RNA recognition motif
Pre-mRNA-splicing factor RDS3 Chain: S
Molecule details ›
Chain: S
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
Sequence domains: PHF5-like protein
Pre-mRNA-splicing factor PRP9 Chain: T
Molecule details ›
Chain: T
Length: 530 amino acids
Theoretical weight: 63.13 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P19736 (Residues: 1-530; Coverage: 100%)
Gene names: D2773, PRP9, YDL030W
Sequence domains:
Pre-mRNA-splicing factor PRP11 Chain: U
Molecule details ›
Chain: U
Length: 266 amino acids
Theoretical weight: 29.29 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q07350 (Residues: 1-266; Coverage: 100%)
Gene names: D2711, PRP10, PRP11, RNA11, YDL043C
Sequence domains:
Pre-mRNA-splicing factor PRP21 Chain: V
Molecule details ›
Chain: V
Length: 280 amino acids
Theoretical weight: 33.11 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P32524 (Residues: 1-280; Coverage: 100%)
Gene names: J0322, PRP21, SPP91, YJL203W
Sequence domains:
Structure domains:
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
Unknown Chain: X
Molecule details ›
Chain: X
Length: 51 amino acids
Theoretical weight: 4.36 KDa
Source organism: Saccharomyces cerevisiae
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
RDS3 complex subunit 10 Chain: Z
Molecule details ›
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
Sequence domains: Splicing factor 3B subunit 10 (SF3b10)
Small nuclear ribonucleoprotein-associated protein B Chains: b, s
Molecule details ›
Chains: b, s
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, v
Molecule details ›
Chains: d, v
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, w
Molecule details ›
Chains: e, w
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, x
Molecule details ›
Chains: f, x
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, y
Molecule details ›
Chains: g, y
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, t
Molecule details ›
Chains: h, t
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
Small nuclear ribonucleoprotein Sm D2 Chains: i, u
Molecule details ›
Chains: i, u
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.
U1 snRNA,U1 snRNA,U1 snRNA,U1 snRNA,U1 snRNA Chain: 1
Molecule details ›
Chain: 1
Length: 407 nucleotides
Theoretical weight: 126.12 KDa
Sequence domains: Yeast U1 spliceosomal RNA
U2 snRNA Chain: 2
Molecule details ›
Chain: 2
Length: 143 nucleotides
Theoretical weight: 45.76 KDa
Sequence domains: U2 spliceosomal RNA
Yeast UBC4 pre-mRNA (mutant) Chain: I
Molecule details ›
Chain: I
Length: 38 nucleotides
Theoretical weight: 12.05 KDa

Ligands and Environments

1 bound ligand:
Ligand ZN 9 x ZN
1 modified residue:
Ligand PSU 5 x PSU

Experiments and Validation Details

Entry percentile scores
Resolution: 4Å
Relevant EMDB volumes: EMD-4364

Quick links

Citations

18 review citations

Splicing and cancer: Challenges and opportunities.
Coltri et al. (2019)
17 more

11 mentions without citation

Structural Basis of Nuclear pre-mRNA Splicing: Lessons from Yeast.
Plaschka et al. (2019)
10 more