› 8q7h

Electron Microscopy
4.1Å resolution

Structure of CUL9-RBX1 ubiquitin E3 ligase complex in unneddylated and neddylated conformation - focused cullin dimer

Released:
DOI: 10.2210/pdb8q7h/pdb
PDB entry 8q7h coloured by chain, front view.
PDB entry 8q7h coloured by chain, side view.
PDB entry 8q7h coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Noncanonical assembly, neddylation and chimeric cullin-RING/RBR ubiquitylation by the 1.8 MDa CUL9 E3 ligase complex.
Horn-Ghetko D, Hopf LVM, Tripathi-Giesgen I, Du J, Kostrhon S, Vu DT, Beier V, Steigenberger B, Prabu JR, Stier L, Bruss EM, Mann M, Xiong Y, Schulman BA
Nat Struct Mol Biol (2024)
PMID: 38605244
Related structures: EMD-18216

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
S-[NEDD8-protein]-yl-[E2 NEDD8-conjugating enzyme]-L-cysteine + [cullin]-L-lysine = [E2 NEDD8-conjugating enzyme]-L-cysteine + N(6)-[NEDD8-protein]-yl-[cullin]-L-lysine
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
PDBe Complex ID:
PDB-CPX-243173 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Cullin-9 Chains: A, B
Molecule details ›
Chains: A, B
Length: 2519 amino acids
Theoretical weight: 281.69 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q8IWT3 (Residues: 1-2517; Coverage: 100%)
Gene names: CUL9, H7AP1, KIAA0708, PARC
Sequence domains:
E3 ubiquitin-protein ligase RBX1 Chains: C, D
Molecule details ›
Chains: C, D
Length: 108 amino acids
Theoretical weight: 12.29 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P62877 (Residues: 1-108; Coverage: 100%)
Gene names: RBX1, RNF75, ROC1
Sequence domains: RING-H2 zinc finger domain
NEDD8 Chain: N
Molecule details ›
Chain: N
Length: 81 amino acids
Theoretical weight: 9.09 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q15843 (Residues: 1-81; Coverage: 100%)
Gene name: NEDD8
Sequence domains: Ubiquitin family
Unknown Chain: E
Molecule details ›
Chain: E
Length: 151 amino acids
Theoretical weight: 12.87 KDa
Source organism: Homo sapiens

Ligands and Environments

1 bound ligand:
Ligand ZN 10 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.1Å
Relevant EMDB volumes: EMD-18216
Expression system: Homo sapiens

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