› 3jb9

Electron Microscopy
3.6Å resolution

Cryo-EM structure of the yeast spliceosome at 3.6 angstrom resolution

Released:
DOI: 10.2210/pdb3jb9/pdb
PDB entry 3jb9 coloured by chain, front view.
PDB entry 3jb9 coloured by chain, side view.
PDB entry 3jb9 coloured by chain, top view.
Source organism: Schizosaccharomyces pombe 972h-
Primary publication:
Structure of a yeast spliceosome at 3.6-angstrom resolution.
Yan C, Hang J, Wan R, Huang M, Wong CC, Shi Y
Science 349 1182-91 (2015)
PMID: 26292707
Related structures: EMD-6413

Function and Biology Details

Reactions catalysed: 
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine
Peptidylproline (omega=180) = peptidylproline (omega=0)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 43-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-126897 (preferred)
Entry contents:
28 distinct polypeptide molecules
5 distinct RNA molecules
Macromolecules (33 distinct):
Pre-mRNA-splicing factor spp42 Chain: A
Molecule details ›
Chain: A
Length: 2363 amino acids
Theoretical weight: 274.92 KDa
Source organism: Schizosaccharomyces pombe 972h-
UniProt:
  • Canonical: O14187 (Residues: 1-2363; Coverage: 100%)
Gene names: SPAC4F8.12c, cwf6, spp42
Sequence domains:
Pre-mRNA-splicing factor cwf10 Chain: B
Molecule details ›
Chain: B
Length: 984 amino acids
Theoretical weight: 111.45 KDa
Source organism: Schizosaccharomyces pombe 972h-
UniProt:
  • Canonical: O94316 (Residues: 1-984; Coverage: 100%)
Gene names: SPBC215.12, cwf10, snu114, spef2
Sequence domains:
Small nuclear ribonucleoprotein Sm D3 Chains: D, Z
Molecule details ›
Chains: D, Z
Length: 97 amino acids
Theoretical weight: 11.05 KDa
Source organism: Schizosaccharomyces pombe 972h-
UniProt:
  • Canonical: Q9UUC6 (Residues: 1-97; Coverage: 100%)
Gene names: SPBC19C2.14, smd3
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
Small nuclear ribonucleoprotein-associated protein B Chains: E, b
Molecule details ›
Chains: E, b
Length: 147 amino acids
Theoretical weight: 15.49 KDa
Source organism: Schizosaccharomyces pombe 972h-
UniProt:
  • Canonical: Q10163 (Residues: 1-147; Coverage: 100%)
Gene names: SPAC26A3.08, smb1
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
Small nuclear ribonucleoprotein Sm D1 Chains: F, f
Molecule details ›
Chains: F, f
Length: 117 amino acids
Theoretical weight: 13.12 KDa
Source organism: Schizosaccharomyces pombe 972h-
UniProt:
  • Canonical: O42661 (Residues: 1-117; Coverage: 100%)
Gene names: SPAC27D7.07c, smd1
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
Small nuclear ribonucleoprotein Sm D2 Chains: G, l
Molecule details ›
Chains: G, l
Length: 115 amino acids
Theoretical weight: 13.12 KDa
Source organism: Schizosaccharomyces pombe 972h-
UniProt:
  • Canonical: O14036 (Residues: 1-115; Coverage: 100%)
Gene names: SPAC2C4.03c, cwf9, smd2
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
Small nuclear ribonucleoprotein E Chains: H, m
Molecule details ›
Chains: H, m
Length: 84 amino acids
Theoretical weight: 9.7 KDa
Source organism: Schizosaccharomyces pombe 972h-
UniProt:
  • Canonical: Q9USZ3 (Residues: 1-84; Coverage: 100%)
Gene names: SPBC11G11.06c, sme1
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
Small nuclear ribonucleoprotein F Chains: I, n
Molecule details ›
Chains: I, n
Length: 78 amino acids
Theoretical weight: 8.67 KDa
Source organism: Schizosaccharomyces pombe 972h-
UniProt:
  • Canonical: O59734 (Residues: 1-78; Coverage: 100%)
Gene names: SPBC3E7.14, SPBC4F6.01, smf1
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
Small nuclear ribonucleoprotein G Chains: J, o
Molecule details ›
Chains: J, o
Length: 77 amino acids
Theoretical weight: 8.62 KDa
Source organism: Schizosaccharomyces pombe 972h-
UniProt:
  • Canonical: O74966 (Residues: 1-77; Coverage: 100%)
Gene names: SPBC4B4.05, smg1
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
Pre-mRNA-splicing factor prp5 Chain: K
Molecule details ›
Chain: K
Length: 473 amino acids
Theoretical weight: 48.91 KDa
Source organism: Schizosaccharomyces pombe 972h-
UniProt:
  • Canonical: O13615 (Residues: 149-473; Coverage: 69%)
Gene names: SPBP22H7.07, cwf1, pi024, prp5
Sequence domains: WD domain, G-beta repeat
Structure domains: YVTN repeat-like/Quinoprotein amine dehydrogenase
Pre-mRNA-splicing factor cwf17 Chain: L
Molecule details ›
Chain: L
Length: 340 amino acids
Theoretical weight: 37.48 KDa
Source organism: Schizosaccharomyces pombe 972h-
UniProt:
  • Canonical: O94620 (Residues: 1-340; Coverage: 100%)
Gene names: SPBC1289.11, cwf17
Sequence domains: WD domain, G-beta repeat
Structure domains: YVTN repeat-like/Quinoprotein amine dehydrogenase
Pre-mRNA-processing protein 45 Chain: M
Molecule details ›
Chain: M
Length: 557 amino acids
Theoretical weight: 62.8 KDa
Source organism: Schizosaccharomyces pombe 972h-
UniProt:
  • Canonical: Q09882 (Residues: 1-557; Coverage: 100%)
Gene names: SPCC188.11, SPCC584.08, cwf13, prp45, snw1
Sequence domains: SKIP/SNW domain
Pre-mRNA-processing factor 19 Chains: S, T, U, V
Molecule details ›
Chains: S, T, U, V
Length: 488 amino acids
Theoretical weight: 54.24 KDa
Source organism: Schizosaccharomyces pombe 972h-
UniProt:
  • Canonical: O14011 (Residues: 1-488; Coverage: 100%)
Gene names: SPAC29A4.08c, cwf8, prp19
Sequence domains:
Structure domains: Zinc/RING finger domain, C3HC4 (zinc finger)
Pre-mRNA-splicing factor cdc5 Chain: W
Molecule details ›
Chain: W
Length: 757 amino acids
Theoretical weight: 75.13 KDa
Source organism: Schizosaccharomyces pombe 972h-
UniProt:
  • Canonical: P39964 (Residues: 1-757; Coverage: 100%)
Gene names: SPAC644.12, cdc5
Sequence domains:
Pre-mRNA-splicing factor cwf2 Chain: Y
Molecule details ›
Chain: Y
Length: 388 amino acids
Theoretical weight: 41.84 KDa
Source organism: Schizosaccharomyces pombe 972h-
UniProt:
  • Canonical: P87126 (Residues: 1-289; Coverage: 75%)
Gene names: SPAC3A12.11c, cwf2, prp3
Sequence domains:
Pre-mRNA-splicing factor cwf5 Chain: a
Molecule details ›
Chain: a
Length: 354 amino acids
Theoretical weight: 37.13 KDa
Source organism: Schizosaccharomyces pombe 972h-
UniProt:
  • Canonical: O59800 (Residues: 1-285; Coverage: 81%)
Gene names: SPCC550.02c, cwf5, ecm2
Sequence domains:
Structure domains: Alpha-Beta Plaits
Pre-mRNA-splicing factor cwf19 Chain: c
Molecule details ›
Chain: c
Length: 639 amino acids
Theoretical weight: 74.55 KDa
Source organism: Schizosaccharomyces pombe 972h-
UniProt:
  • Canonical: Q09909 (Residues: 1-639; Coverage: 100%)
Gene names: SPAC30D11.09, cwf19
Sequence domains:
Peptidyl-prolyl cis-trans isomerase ppi1 Chain: d
Molecule details ›
Chain: d
Length: 155 amino acids
Theoretical weight: 16.88 KDa
Source organism: Schizosaccharomyces pombe 972h-
UniProt:
  • Canonical: P87051 (Residues: 1-155; Coverage: 100%)
Gene names: SPAC57A10.03, cyp2, ppi1
Sequence domains: Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD
Structure domains: Cyclophilin-like
Pre-mRNA-splicing factor cwf14 Chain: e
Molecule details ›
Chain: e
Length: 146 amino acids
Theoretical weight: 17.12 KDa
Source organism: Schizosaccharomyces pombe 972h-
UniProt:
  • Canonical: O74772 (Residues: 1-146; Coverage: 100%)
Gene names: SPBC24C6.11, cwf14
Sequence domains: Pre-mRNA-splicing factor BUD31
Pre-mRNA-processing factor 17 Chain: g
Molecule details ›
Chain: g
Length: 558 amino acids
Theoretical weight: 63.21 KDa
Source organism: Schizosaccharomyces pombe 972h-
UniProt:
  • Canonical: O43071 (Residues: 1-558; Coverage: 100%)
Gene names: SPBC6B1.10, prp17
Sequence domains: WD domain, G-beta repeat
Pre-mRNA-splicing factor cwf15 Chain: h
Molecule details ›
Chain: h
Length: 265 amino acids
Theoretical weight: 30.48 KDa
Source organism: Schizosaccharomyces pombe 972h-
UniProt:
  • Canonical: P78794 (Residues: 1-265; Coverage: 100%)
Gene names: SPBC337.06c, cwf15
Sequence domains: Cwf15/Cwc15 cell cycle control protein
Pre-mRNA-splicing factor cwf7 Chain: i
Molecule details ›
Chain: i
Length: 187 amino acids
Theoretical weight: 21.35 KDa
Source organism: Schizosaccharomyces pombe 972h-
UniProt:
  • Canonical: Q9USV3 (Residues: 1-187; Coverage: 100%)
Gene names: SPBC28F2.04c, cwf7, spf27
Sequence domains: Breast carcinoma amplified sequence 2 (BCAS2)
Pre-mRNA-splicing factor cwf4 Chain: R
Molecule details ›
Chain: R
Length: 674 amino acids
Theoretical weight: 67.08 KDa
Source organism: Schizosaccharomyces pombe 972h-
UniProt:
  • Canonical: P87312 (Residues: 41-290; Coverage: 37%)
Gene names: SPBC31F10.11c, cwf4, syf3
Sequence domains:
Pre-mRNA-splicing factor cwf3 Chain: r
Molecule details ›
Chain: r
Length: 790 amino acids
Theoretical weight: 72.17 KDa
Source organism: Schizosaccharomyces pombe 972h-
UniProt:
  • Canonical: Q9P7R9 (Residues: 498-653; Coverage: 20%)
Gene names: SPBC211.02c, cwf3, syf1
Pre-mRNA-splicing factor cwf11 Chain: X
Molecule details ›
Chain: X
Length: 1284 amino acids
Theoretical weight: 148.53 KDa
Source organism: Schizosaccharomyces pombe 972h-
UniProt:
  • Canonical: O94508 (Residues: 1-1284; Coverage: 100%)
Gene names: SPBC646.02, cwf11
Sequence domains:
U2 small nuclear ribonucleoprotein A' Chain: j
Molecule details ›
Chain: j
Length: 239 amino acids
Theoretical weight: 27.26 KDa
Source organism: Schizosaccharomyces pombe 972h-
UniProt:
  • Canonical: Q9USX8 (Residues: 1-239; Coverage: 100%)
Gene names: SPBC1861.08c, lea1
Sequence domains: Leucine Rich repeats (2 copies)
Structure domains: Ribonuclease Inhibitor
Probable U2 small nuclear ribonucleoprotein B'' Chain: k
Molecule details ›
Chain: k
Length: 111 amino acids
Theoretical weight: 12.69 KDa
Source organism: Schizosaccharomyces pombe 972h-
UniProt:
  • Canonical: Q7LL14 (Residues: 1-111; Coverage: 100%)
Gene names: SPBC8D2.09c, msl1, pi056
Sequence domains: RNA recognition motif
Structure domains: Alpha-Beta Plaits
unknown chain Chain: x
Molecule details ›
Chain: x
Length: 412 amino acids
Theoretical weight: 35.08 KDa
Source organism: Schizosaccharomyces pombe 972h-
U5 snRNA Chain: C
Molecule details ›
Chain: C
Length: 120 nucleotides
Theoretical weight: 38.19 KDa
Sequence domains: U5 spliceosomal RNA
U6 snRNA Chain: N
Molecule details ›
Chain: N
Length: 99 nucleotides
Theoretical weight: 31.86 KDa
Sequence domains: U6 spliceosomal RNA
RNA (5'-R(P*GP*UP*AP*UP*GP*UP*AP*U)-3') Chain: O
Molecule details ›
Chain: O
Length: 8 nucleotides
Theoretical weight: 2.53 KDa
RNA (5'-R(P*UP*UP*UP*AP*UP*AP*CP*UP*AP*AP*CP*AP*C)-3') Chain: Q
Molecule details ›
Chain: Q
Length: 13 nucleotides
Theoretical weight: 4.05 KDa
U2 snRNA Chain: P
Molecule details ›
Chain: P
Length: 186 nucleotides
Theoretical weight: 59.21 KDa
Sequence domains: U2 spliceosomal RNA

Ligands and Environments

4 bound ligands:
Ligand GDP 1 x GDP
Ligand MG 4 x MG
Ligand ZN 7 x ZN
Ligand ADP 1 x ADP
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.6Å
Relevant EMDB volumes: EMD-6413

Quick links

Citations

67 review citations

Therapeutic targeting of splicing in cancer.
Lee et al. (2016)
66 more

29 mentions without citation

Cryo-electron microscopy snapshots of the spliceosome: structural insights into a dynamic ribonucleoprotein machine.
Fica et al. (2017)
28 more