› 8wjn

Electron Microscopy
5.58Å resolution

Cryo-EM structure of 6-subunit Smc5/6 head region

Released:
DOI: 10.2210/pdb8wjn/pdb
PDB entry 8wjn coloured by chain, front view.
PDB entry 8wjn coloured by chain, side view.
PDB entry 8wjn coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Cryo-EM structures of Smc5/6 in multiple states reveal its assembly and functional mechanisms.
Li Q, Zhang J, Haluska C, Zhang X, Wang L, Liu G, Wang Z, Jin D, Cheng T, Wang H, Tian Y, Wang X, Sun L, Zhao X, Chen Z, Wang L
Nat Struct Mol Biol (2024)
PMID: 38890552
Related structures: EMD-37586

Function and Biology Details

Reaction 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
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
PDBe Complex ID:
PDB-CPX-246196 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (5 distinct):
Structural maintenance of chromosomes protein 6 Chain: B
Molecule details ›
Chain: B
Length: 1114 amino acids
Theoretical weight: 128.2 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q12749 (Residues: 1-1114; Coverage: 100%)
Gene names: L3502.2, RHC18, SMC6, YLR383W
Sequence domains: AAA domain
Structural maintenance of chromosomes protein 5 Chain: A
Molecule details ›
Chain: A
Length: 1093 amino acids
Theoretical weight: 126.24 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q08204 (Residues: 1-1093; Coverage: 100%)
Gene names: SMC5, YOL034W
Sequence domains: RecF/RecN/SMC N terminal domain
Non-structural maintenance of chromosomes element 1 Chain: F
Molecule details ›
Chain: F
Length: 336 amino acids
Theoretical weight: 38.37 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q07913 (Residues: 1-336; Coverage: 100%)
Gene names: NSE1, YLR007W
Sequence domains:
Non-structural maintenance of chromosome element 3 Chain: G
Molecule details ›
Chain: G
Length: 303 amino acids
Theoretical weight: 34.01 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q05541 (Residues: 1-303; Coverage: 100%)
Gene names: NSE3, YDR288W
Sequence domains: MAGE homology domain
Non-structural maintenance of chromosomes element 4 Chain: H
Molecule details ›
Chain: H
Length: 402 amino acids
Theoretical weight: 46.2 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: A0A6L0Z6W9 (Residues: 1-402; Coverage: 100%)
Gene names: GI527_G0000825, NSE4
Sequence domains:

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 5.58Å
Relevant EMDB volumes: EMD-37586
Expression system: Spodoptera frugiperda

Quick links