› 5n4w

X-ray diffraction
3.9Å resolution

Crystal structure of the Cul2-Rbx1-EloBC-VHL ubiquitin ligase complex

Released:
DOI: 10.2210/pdb5n4w/pdb
PDB entry 5n4w coloured by chain, front view.
PDB entry 5n4w coloured by chain, side view.
PDB entry 5n4w coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal Structure of the Cul2-Rbx1-EloBC-VHL Ubiquitin Ligase Complex.
Cardote TAF, Gadd MS, Ciulli A
Structure 25 901-911.e3 (2017)
PMID: 28591624

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:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-154081 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (5 distinct):
Cullin-2 Chain: A
Molecule details ›
Chain: A
Length: 748 amino acids
Theoretical weight: 87.3 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q13617 (Residues: 1-745; Coverage: 100%)
Gene name: CUL2
Sequence domains:
von Hippel-Lindau disease tumor suppressor Chain: V
Molecule details ›
Chain: V
Length: 160 amino acids
Theoretical weight: 18.56 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P40337 (Residues: 54-213; Coverage: 75%)
Gene name: VHL
Sequence domains:
E3 ubiquitin-protein ligase RBX1 Chain: R
Molecule details ›
Chain: R
Length: 102 amino acids
Theoretical weight: 11.6 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P62877 (Residues: 1-102; Coverage: 94%)
Gene names: RBX1, RNF75, ROC1
Sequence domains: RING-H2 zinc finger domain
Elongin-B Chain: B
Molecule details ›
Chain: B
Length: 104 amino acids
Theoretical weight: 11.75 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q15370 (Residues: 1-104; Coverage: 88%)
Gene names: ELOB, TCEB2
Sequence domains: Ubiquitin family
Structure domains: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Elongin-C Chain: C
Molecule details ›
Chain: C
Length: 97 amino acids
Theoretical weight: 10.97 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q15369 (Residues: 17-112; Coverage: 86%)
Gene names: ELOC, TCEB1
Sequence domains: Skp1 family, tetramerisation domain
Structure domains: Potassium Channel Kv1.1; Chain A

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: C2221
Unit cell:
a: 86.038Å b: 190.962Å c: 238.885Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.304 0.302 0.346
Expression systems:
  • Spodoptera frugiperda
  • Escherichia coli

Quick links

Citations

18 review citations

Degradation of proteins by PROTACs and other strategies.
Wang et al. (2020)
17 more

19 mentions without citation

Proteolysis-Targeting Chimeras as Therapeutics and Tools for Biological Discovery.
Burslem et al. (2020)
18 more