› 6n7p

Electron Microscopy
3.6Å resolution

S. cerevisiae spliceosomal E complex (UBC4)

Released:
DOI: 10.2210/pdb6n7p/pdb
PDB entry 6n7p coloured by chain, front view.
PDB entry 6n7p coloured by chain, side view.
PDB entry 6n7p coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
A unified mechanism for intron and exon definition and back-splicing.
Li X, Liu S, Zhang L, Issaian A, Hill RC, Espinosa S, Shi S, Cui Y, Kappel K, Das R, Hansen KC, Zhou ZH, Zhao R
Nature 573 375-380 (2019)
PMID: 31485080
Related structures: EMD-0360

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 21-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-152394 (preferred)
Entry contents:
19 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (21 distinct):
U1 small nuclear ribonucleoprotein 70 kDa homolog Chain: A
Molecule details ›
Chain: A
Length: 300 amino acids
Theoretical weight: 34.51 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q00916 (Residues: 1-300; Coverage: 100%)
Gene names: SNP1, YIL061C
Sequence domains:
U1 small nuclear ribonucleoprotein C Chain: B
Molecule details ›
Chain: B
Length: 231 amino acids
Theoretical weight: 27.11 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q05900 (Residues: 1-231; Coverage: 100%)
Gene names: L8003.21, YHC1, YLR298C
Sequence domains: U1 zinc finger
U1 small nuclear ribonucleoprotein A Chain: C
Molecule details ›
Chain: C
Length: 350 amino acids
Theoretical weight: 40.41 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P32605 (Residues: 1-298; Coverage: 100%)
Gene names: MUD1, YBR0915, YBR119W
Sequence domains: RNA recognition motif
U1 small nuclear ribonucleoprotein component PRP42 Chain: D
Molecule details ›
Chain: D
Length: 544 amino acids
Theoretical weight: 65.22 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q03776 (Residues: 1-544; Coverage: 100%)
Gene names: MUD16, PRP42, SNU65, YD8419.02, YDR235W
Pre-mRNA-processing factor 39 Chain: E
Molecule details ›
Chain: E
Length: 629 amino acids
Theoretical weight: 74.83 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P39682 (Residues: 1-629; Coverage: 100%)
Gene names: PRP39, YM9827.06, YML046W
Protein NAM8 Chain: F
Molecule details ›
Chain: F
Length: 523 amino acids
Theoretical weight: 57.01 KDa
Source organism: Saccharomyces cerevisiae S288C
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 S288C
UniProt:
  • Canonical: Q03782 (Residues: 1-492; Coverage: 100%)
Gene names: MUD10, SNU56, YDR240C
Sequence domains: Snu56-like U1 small nuclear ribonucleoprotein component
U1 small nuclear ribonucleoprotein component SNU71 Chain: H
Molecule details ›
Chain: H
Length: 105 amino acids
Theoretical weight: 10.49 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P53207 (Residues: 1-52; Coverage: 8%)
Gene names: SNU71, YGR013W
Protein LUC7 Chain: I
Molecule details ›
Chain: I
Length: 261 amino acids
Theoretical weight: 30.25 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q07508 (Residues: 1-261; Coverage: 100%)
Gene names: EPE1, EXM2, LUC7, YDL087C
Sequence domains: LUC7 N_terminus
Pre-mRNA-processing protein PRP40 Chain: J
Molecule details ›
Chain: J
Length: 583 amino acids
Theoretical weight: 69.18 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P33203 (Residues: 1-583; Coverage: 100%)
Gene names: PRP40, YKL012W, YKL165
Sequence domains:
Small nuclear ribonucleoprotein-associated protein B Chain: K
Molecule details ›
Chain: K
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
Sequence domains: LSM domain
Small nuclear ribonucleoprotein Sm D1 Chain: L
Molecule details ›
Chain: L
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
Sequence domains: LSM domain
Small nuclear ribonucleoprotein Sm D2 Chain: M
Molecule details ›
Chain: M
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
Sequence domains: LSM domain
Small nuclear ribonucleoprotein Sm D3 Chain: N
Molecule details ›
Chain: N
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
Sequence domains: LSM domain
Small nuclear ribonucleoprotein E Chain: O
Molecule details ›
Chain: O
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
Sequence domains: LSM domain
Small nuclear ribonucleoprotein F Chain: P
Molecule details ›
Chain: P
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
Sequence domains: LSM domain
Small nuclear ribonucleoprotein G Chain: Q
Molecule details ›
Chain: Q
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
Sequence domains: LSM domain
Nuclear cap-binding protein complex subunit 1 Chain: X
Molecule details ›
Chain: X
Length: 861 amino acids
Theoretical weight: 100.12 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P34160 (Residues: 1-861; Coverage: 100%)
Gene names: CBC1, CBP80, GCR3, STO1, SUT1, YM8564.07, YM9553.01, YMR125W
Sequence domains:
Nuclear cap-binding protein subunit 2 Chain: Y
Molecule details ›
Chain: Y
Length: 208 amino acids
Theoretical weight: 23.8 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q08920 (Residues: 1-208; Coverage: 100%)
Gene names: CBC2, CBP20, MUD13, SAE1, YPL178W
Sequence domains: RNA recognition motif
U1 snRNA Chain: R
Molecule details ›
Chain: R
Length: 568 nucleotides
Theoretical weight: 182.11 KDa
Sequence domains: Yeast U1 spliceosomal RNA
UBC4 pre-mRNA Chain: r
Molecule details ›
Chain: r
Length: 253 nucleotides
Theoretical weight: 81.03 KDa

Ligands and Environments

1 bound ligand:
Ligand ZN 3 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.6Å
Relevant EMDB volumes: EMD-0360
Expression system: Saccharomyces cerevisiae S288C

Quick links

Citations

36 review citations

The expanding regulatory mechanisms and cellular functions of circular RNAs.
Chen LL. (2020)
35 more

2 mentions without citation

A unified mechanism for intron and exon definition and back-splicing.
Li et al. (2019)
1 more