› 8pql

Electron Microscopy
3.76Å resolution

K48-linked ubiquitin chain formation with a cullin-RING E3 ligase and Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2-donor UB-acceptor UB-SIL1 peptide

Released:
DOI: 10.2210/pdb8pql/pdb
PDB entry 8pql coloured by chain, front view.
PDB entry 8pql coloured by chain, side view.
PDB entry 8pql coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Mechanism of millisecond Lys48-linked poly-ubiquitin chain formation by cullin-RING ligases.
Liwocha J, Li J, Purser N, Rattanasopa C, Maiwald S, Krist DT, Scott DC, Steigenberger B, Prabu JR, Schulman BA, Kleiger G
Nat Struct Mol Biol (2024)
PMID: 38326650
Related structures: EMD-17822

Function and Biology Details

Reactions catalysed: 
S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine
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 octamer (preferred)
PDBe Complex ID:
PDB-CPX-239925 (preferred)
Entry contents:
8 distinct polypeptide molecules
Macromolecules (8 distinct):
Ubiquitin-conjugating enzyme E2 R2 Chain: C
Molecule details ›
Chain: C
Length: 238 amino acids
Theoretical weight: 27.19 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q712K3 (Residues: 1-238; Coverage: 100%)
Gene names: CDC34B, UBC3B, UBE2R2
Sequence domains: Ubiquitin-conjugating enzyme
Nucleotide exchange factor SIL1; Polyubiquitin-C Chain: E
Molecule details ›
Chain: E
Length: 704 amino acids
Theoretical weight: 79.23 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P0CG48 (Residues: 1-685; Coverage: 100%)
  • Canonical: Q9H173 (Residues: 443-461; Coverage: 4%)
Gene names: SIL1, UBC, UNQ545/PRO836
Sequence domains: Ubiquitin family
Protein fem-1 homolog C Chain: H
Molecule details ›
Chain: H
Length: 617 amino acids
Theoretical weight: 68.77 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q96JP0 (Residues: 1-617; Coverage: 100%)
Gene names: FEM1C, KIAA1785
Sequence domains: Ankyrin repeats (3 copies)
E3 ubiquitin-protein ligase RBX1 Chain: K
Molecule details ›
Chain: K
Length: 108 amino acids
Theoretical weight: 12.29 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P62877 (Residues: 1-108; Coverage: 100%)
Gene names: RBX1, RNF75, ROC1
Sequence domains: RING-H2 zinc finger domain
Polyubiquitin-C Chain: U
Molecule details ›
Chain: U
Length: 685 amino acids
Theoretical weight: 77.12 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P0CG48 (Residues: 1-685; Coverage: 100%)
Gene name: UBC
Sequence domains: Ubiquitin family
Cullin-2 Chain: A
Molecule details ›
Chain: A
Length: 745 amino acids
Theoretical weight: 87.1 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q13617 (Residues: 1-745; Coverage: 100%)
Gene name: CUL2
Sequence domains:
Elongin-C Chain: D
Molecule details ›
Chain: D
Length: 112 amino acids
Theoretical weight: 12.49 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q15369 (Residues: 1-112; Coverage: 100%)
Gene names: ELOC, TCEB1
Sequence domains: Skp1 family, tetramerisation domain
Elongin-B Chain: G
Molecule details ›
Chain: G
Length: 118 amino acids
Theoretical weight: 13.15 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q15370 (Residues: 1-118; Coverage: 100%)
Gene names: ELOB, TCEB2
Sequence domains: Ubiquitin family

Ligands and Environments

2 bound ligands:
Ligand SY8 1 x SY8
Ligand ZN 3 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.76Å
Relevant EMDB volumes: EMD-17822
Expression systems:
  • Escherichia coli BL21
  • Trichoplusia ni

Quick links

Citations

1 mention without citation

Mechanism of millisecond Lys48-linked poly-ubiquitin chain formation by cullin-RING ligases.
Liwocha et al. (2024)