9esh

Electron Microscopy
3.2Å resolution

Structure of a B-state intermediate committed to discard (Bd-I state)

Released:

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)
ATP + H(2)O = ADP + phosphate
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero 39-mer (preferred)
PDBe Complex ID:
PDB-CPX-283157 (preferred)
Entry contents:
32 distinct polypeptide molecules
4 distinct RNA molecules
Macromolecules (36 distinct):
Pre-mRNA-splicing factor spp42 Chain: A
Pre-mRNA-splicing factor cwf10 Chain: B
Molecule details ›
Chain: B
Length: 984 amino acids
Theoretical weight: 111.45 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: O94316 (Residues: 1-984; Coverage: 100%)
Gene names: SPBC215.12, cwf10, snu114, spef2
Sequence domains:
Pre-mRNA-splicing factor cwf17 Chain: C
Molecule details ›
Chain: C
Length: 340 amino acids
Theoretical weight: 37.48 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: O94620 (Residues: 1-340; Coverage: 100%)
Gene names: SPBC1289.11, cwf17
Sequence domains: WD domain, G-beta repeat
Small nuclear ribonucleoprotein Sm D3 Chain: D
Molecule details ›
Chain: D
Length: 97 amino acids
Theoretical weight: 11.05 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: Q9UUC6 (Residues: 1-97; Coverage: 100%)
Gene names: SPBC19C2.14, smd3
Sequence domains: LSM domain
Small nuclear ribonucleoprotein-associated protein B Chain: E
Molecule details ›
Chain: E
Length: 147 amino acids
Theoretical weight: 15.49 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: Q10163 (Residues: 1-147; Coverage: 100%)
Gene names: SPAC26A3.08, smb1
Sequence domains: LSM domain
Small nuclear ribonucleoprotein Sm D1 Chain: F
Molecule details ›
Chain: F
Length: 117 amino acids
Theoretical weight: 13.12 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: O42661 (Residues: 1-117; Coverage: 100%)
Gene names: SPAC27D7.07c, smd1
Sequence domains: LSM domain
Small nuclear ribonucleoprotein Sm D2 Chain: G
Molecule details ›
Chain: G
Length: 115 amino acids
Theoretical weight: 13.12 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: O14036 (Residues: 1-115; Coverage: 100%)
Gene names: SPAC2C4.03c, cwf9, smd2
Sequence domains: LSM domain
Small nuclear ribonucleoprotein E Chain: H
Molecule details ›
Chain: H
Length: 84 amino acids
Theoretical weight: 9.7 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: Q9USZ3 (Residues: 1-84; Coverage: 100%)
Gene names: SPBC11G11.06c, sme1
Sequence domains: LSM domain
Small nuclear ribonucleoprotein F Chain: I
Molecule details ›
Chain: I
Length: 78 amino acids
Theoretical weight: 8.67 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: O59734 (Residues: 1-78; Coverage: 100%)
Gene names: SPBC3E7.14, SPBC4F6.01, smf1
Sequence domains: LSM domain
Small nuclear ribonucleoprotein G Chain: J
Molecule details ›
Chain: J
Length: 77 amino acids
Theoretical weight: 8.62 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: O74966 (Residues: 1-77; Coverage: 100%)
Gene names: SPBC4B4.05, smg1
Sequence domains: LSM domain
Pre-mRNA-splicing factor prp5 Chain: K
Molecule details ›
Chain: K
Length: 473 amino acids
Theoretical weight: 52.49 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: O13615 (Residues: 1-473; Coverage: 100%)
Gene names: SPBP22H7.07, cwf1, pi024, prp5
Sequence domains: WD domain, G-beta repeat
Pre-mRNA-processing protein 45 Chain: L
Molecule details ›
Chain: L
Length: 557 amino acids
Theoretical weight: 62.8 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: Q09882 (Residues: 1-557; Coverage: 100%)
Gene names: SPCC188.11, SPCC584.08, cwf13, prp45, snw1
Sequence domains: SKIP/SNW domain
Pre-mRNA-splicing factor cwf5 Chain: M
Molecule details ›
Chain: M
Length: 354 amino acids
Theoretical weight: 39.64 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: O59800 (Residues: 1-354; Coverage: 100%)
Gene names: SPCC550.02c, cwf5, ecm2
Sequence domains:
Pre-mRNA-splicing factor cwf11 Chain: N
Molecule details ›
Chain: N
Length: 1284 amino acids
Theoretical weight: 148.53 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: O94508 (Residues: 1-1284; Coverage: 100%)
Gene names: SPBC646.02, cwf11
Sequence domains:
Pre-mRNA-splicing factor cwf14 Chain: O
Molecule details ›
Chain: O
Length: 146 amino acids
Theoretical weight: 17.12 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: O74772 (Residues: 1-146; Coverage: 100%)
Gene names: SPBC24C6.11, cwf14
Sequence domains: Pre-mRNA-splicing factor BUD31
Pre-mRNA-splicing factor cwf2 Chain: P
Molecule details ›
Chain: P
Length: 388 amino acids
Theoretical weight: 44.34 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: P87126 (Residues: 1-388; Coverage: 100%)
Gene names: SPAC3A12.11c, cwf2, prp3
Sequence domains:
Pre-mRNA-splicing factor cwf15 Chain: Q
Molecule details ›
Chain: Q
Length: 265 amino acids
Theoretical weight: 30.48 KDa
Source organism: Schizosaccharomyces pombe
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 cwf4 Chain: R
Molecule details ›
Chain: R
Length: 674 amino acids
Theoretical weight: 80.96 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: P87312 (Residues: 1-674; Coverage: 100%)
Gene names: SPBC31F10.11c, cwf4, syf3
Sequence domains:
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
UniProt:
  • Canonical: O14011 (Residues: 1-488; Coverage: 100%)
Gene names: SPAC29A4.08c, cwf8, prp19
Sequence domains:
Pre-mRNA-splicing factor cdc5 Chain: W
Molecule details ›
Chain: W
Length: 757 amino acids
Theoretical weight: 86.98 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: P39964 (Residues: 1-757; Coverage: 100%)
Gene names: SPAC644.12, cdc5
Sequence domains:
Pre-mRNA-splicing factor cwf3 Chain: X
Molecule details ›
Chain: X
Length: 790 amino acids
Theoretical weight: 92.76 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: Q9P7R9 (Residues: 1-790; Coverage: 100%)
Gene names: SPBC211.02c, cwf3, syf1
Sequence domains: Suppressor of forked protein (Suf)
Pre-mRNA-splicing factor syf2 Chain: Y
Molecule details ›
Chain: Y
Length: 229 amino acids
Theoretical weight: 28.04 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: O59733 (Residues: 1-229; Coverage: 100%)
Gene names: SPBC3E7.13c, syf2
Sequence domains: SYF2 splicing factor
Pre-mRNA-splicing factor cwf7 Chain: Z
Molecule details ›
Chain: Z
Length: 187 amino acids
Theoretical weight: 21.35 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: Q9USV3 (Residues: 1-187; Coverage: 100%)
Gene names: SPBC28F2.04c, cwf7, spf27
Sequence domains: Breast carcinoma amplified sequence 2 (BCAS2)
Pre-mRNA-processing factor 17 Chain: a
Molecule details ›
Chain: a
Length: 558 amino acids
Theoretical weight: 63.21 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: O43071 (Residues: 1-558; Coverage: 100%)
Gene names: SPBC6B1.10, prp17
Sequence domains: WD domain, G-beta repeat
Pre-mRNA-splicing factor cwf21 Chain: b
Molecule details ›
Chain: b
Length: 293 amino acids
Theoretical weight: 34.62 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: O14161 (Residues: 1-293; Coverage: 100%)
Gene names: SPAC4A8.09c, cwf21
Sequence domains: cwf21 domain
Pre-mRNA-splicing factor cwf22 Chain: c
Molecule details ›
Chain: c
Length: 887 amino acids
Theoretical weight: 102.93 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: Q9P6R9 (Residues: 1-887; Coverage: 100%)
Gene names: SPBC13E7.01, SPBC15D4.16, cwf22
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
UniProt:
  • Canonical: P87051 (Residues: 1-155; Coverage: 100%)
Gene names: SPAC57A10.03, cyp2, ppi1
Sequence domains: Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD
UNK1 Chain: f
Molecule details ›
Chain: f
Length: 22 amino acids
Theoretical weight: 1.89 KDa
Source organism: Schizosaccharomyces pombe
G-patch domain-containing protein C1486.03 Chain: m
Molecule details ›
Chain: m
Length: 797 amino acids
Theoretical weight: 91.79 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: Q9UTK6 (Residues: 1-797; Coverage: 100%)
Gene name: SPAC1486.03c
Sequence domains:
UNK2 Chain: r
Molecule details ›
Chain: r
Length: 346 amino acids
Theoretical weight: 29.46 KDa
Source organism: Schizosaccharomyces pombe
Uncharacterized protein C20H4.06c Chain: y
Molecule details ›
Chain: y
Length: 534 amino acids
Theoretical weight: 60.85 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: Q9HE07 (Residues: 1-534; Coverage: 100%)
Gene name: SPAC20H4.06c
Sequence domains: Protein of unknown function (DUF1604)
Putative pre-mRNA-splicing factor ATP-dependent RNA helicase C20H4.09 Chain: z
pre-mRNA Chain: 1
Molecule details ›
Chain: 1
Length: 29 nucleotides
Theoretical weight: 9.14 KDa
U2snRNA Chain: 2
Molecule details ›
Chain: 2
Length: 186 nucleotides
Theoretical weight: 59.21 KDa
U5snRNA Chain: 5
Molecule details ›
Chain: 5
Length: 120 nucleotides
Theoretical weight: 38.19 KDa
U6snRNA Chain: 6
Molecule details ›
Chain: 6
Length: 99 nucleotides
Theoretical weight: 31.86 KDa

Ligands and Environments

No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.2Å
Relevant EMDB volumes: EMD-19941