› 8qhc

Electron Microscopy
3.1Å resolution

Cryo-EM structure of SidH from Legionella pneumophila in complex with LubX

Released:
DOI: 10.2210/pdb8qhc/pdb
PDB entry 8qhc coloured by chain, front view.
PDB entry 8qhc coloured by chain, side view.
PDB entry 8qhc coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis for the toxicity of Legionella pneumophila effector SidH.
Sharma R, Adams M, Griffith-Jones S, Sahr T, Gomez-Valero L, Weis F, Hons M, Gharbi S, Berkane R, Stolz A, Buchrieser C, Bhogaraju S
OpenAccess logo Nat Commun 14 7068 (2023)
PMID: 37923743
Related structures: EMD-18407

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:
Biological process:
Cellular component:
Sequence domain:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-533693 (preferred)
Entry contents:
3 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (4 distinct):
Elongation factor Tu 2 Chain: C
Molecule details ›
Chain: C
Length: 394 amino acids
Theoretical weight: 43.37 KDa
Source organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: P0CE48 (Residues: 1-394; Coverage: 100%)
Gene names: JW3943, b3980, tufB
Sequence domains:
SidH Chain: A
Molecule details ›
Chain: A
Length: 2244 amino acids
Theoretical weight: 255.11 KDa
Source organism: Legionella pneumophila
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: Q6RCQ4 (Residues: 1-2225; Coverage: 100%)
E3 ubiquitin-protein ligase LubX Chain: D
Molecule details ›
Chain: D
Length: 264 amino acids
Theoretical weight: 30.51 KDa
Source organism: Legionella pneumophila
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5ZRQ0 (Residues: 1-246; Coverage: 100%)
Gene names: legU2, lpg2830, lubX
Sequence domains: U-box domain
t-RNA Chain: B
Molecule details ›
Chain: B
Length: 76 nucleotides
Theoretical weight: 24.62 KDa
Sequence domains: tRNA

Ligands and Environments

2 bound ligands:
Ligand MG 1 x MG
Ligand GTP 1 x GTP
5 modified residues:
Ligand 4SU 1 x 4SU
Ligand H2U 2 x H2U
Ligand 3AU 1 x 3AU
Ligand 5MU 1 x 5MU
Ligand PSU 1 x PSU

Experiments and Validation Details

Entry percentile scores
Resolution: 3.1Å
Relevant EMDB volumes: EMD-18407
Expression systems:
  • Escherichia coli 'BL21-Gold(DE3)pLysS AG'
  • Escherichia coli

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