› 5zwn

Electron Microscopy
3.4Å resolution

Cryo-EM structure of the yeast pre-B complex at an average resolution of 3.3 angstrom (Part II: U1 snRNP region)

Released:
DOI: 10.2210/pdb5zwn/pdb
PDB entry 5zwn coloured by chain, front view.
PDB entry 5zwn coloured by chain, side view.
PDB entry 5zwn coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Structures of the fully assembled Saccharomyces cerevisiae spliceosome before activation.
Bai R, Wan R, Yan C, Lei J, Shi Y
Science 360 1423-1429 (2018)
PMID: 29794219
Related structures: EMD-6973

Function and Biology Details

Reaction catalysed: 
ATP + H(2)O = ADP + phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero icosamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-149949 (preferred)
Entry contents:
18 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (20 distinct):
U1 small nuclear ribonucleoprotein 70 kDa homolog Chain: Q
Molecule details ›
Chain: Q
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: R
Molecule details ›
Chain: R
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: S
Molecule details ›
Chain: S
Length: 298 amino acids
Theoretical weight: 34.44 KDa
Source organism: 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: T
Molecule details ›
Chain: T
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: U
Molecule details ›
Chain: U
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: V
Molecule details ›
Chain: V
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: W
Molecule details ›
Chain: W
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
Small nuclear ribonucleoprotein-associated protein B Chain: a
Molecule details ›
Chain: a
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: b
Molecule details ›
Chain: b
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: c
Molecule details ›
Chain: c
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
Structure domains: SH3 type barrels.
Small nuclear ribonucleoprotein Sm D3 Chain: d
Molecule details ›
Chain: d
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
Structure domains: SH3 type barrels.
Small nuclear ribonucleoprotein E Chain: e
Molecule details ›
Chain: e
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
Structure domains: SH3 type barrels.
Small nuclear ribonucleoprotein F Chain: f
Molecule details ›
Chain: f
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
Structure domains: SH3 type barrels.
Small nuclear ribonucleoprotein G Chain: g
Molecule details ›
Chain: g
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
Structure domains: SH3 type barrels.
U1 small nuclear ribonucleoprotein component SNU71 Chain: X
Molecule details ›
Chain: X
Length: 619 amino acids
Theoretical weight: 71.38 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P53207 (Residues: 1-619; Coverage: 100%)
Gene names: SNU71, YGR013W
Protein LUC7 Chain: Y
Molecule details ›
Chain: Y
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
U1 snRNP Chain: x
Molecule details ›
Chain: x
Length: 49 amino acids
Theoretical weight: 3.5 KDa
Source organism: Saccharomyces cerevisiae S288C
Structure domains: Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Pre-mRNA-splicing ATP-dependent RNA helicase PRP28 Chain: y
Molecule details ›
Chain: y
Length: 588 amino acids
Theoretical weight: 66.73 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P23394 (Residues: 1-588; Coverage: 100%)
Gene names: PRP28, YD8419.10C, YDR243C
Sequence domains:
pre-mRNA Chain: G
Molecule details ›
Chain: G
Length: 22 nucleotides
Theoretical weight: 7.13 KDa
U1 snRNA Chain: P
Molecule details ›
Chain: P
Length: 568 nucleotides
Theoretical weight: 182.11 KDa
Sequence domains: Yeast U1 spliceosomal RNA

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
Resolution: 3.4Å
Relevant EMDB volumes: EMD-6973

Quick links

Citations

10 review citations

Roles and mechanisms of alternative splicing in cancer - implications for care.
Bonnal et al. (2020)
9 more

3 mentions without citation

Structural insights into how Prp5 proofreads the pre-mRNA branch site.
Zhang et al. (2021)
2 more