› 5o76

X-ray diffraction
2.47Å resolution

Structure of phosphoY371 c-CBL in complex with ZAP70-peptide and UbV.pCBL ubiquitin variant

Released:
DOI: 10.2210/pdb5o76/pdb
PDB entry 5o76 coloured by chain, front view.
PDB entry 5o76 coloured by chain, side view.
PDB entry 5o76 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
A General Strategy for Discovery of Inhibitors and Activators of RING and U-box E3 Ligases with Ubiquitin Variants.
Gabrielsen M, Buetow L, Nakasone MA, Ahmed SF, Sibbet GJ, Smith BO, Zhang W, Sidhu SS, Huang DT
Mol Cell 68 456-470.e10 (2017)
PMID: 29053960

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
ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-149760 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
E3 ubiquitin-protein ligase CBL Chains: A, C
Molecule details ›
Chains: A, C
Length: 391 amino acids
Theoretical weight: 45.14 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P22681 (Residues: 47-435; Coverage: 43%)
Gene names: CBL, CBL2, RNF55
Sequence domains:
Structure domains:
Tyrosine-protein kinase ZAP-70 Chains: B, D
Molecule details ›
Chains: B, D
Length: 12 amino acids
Theoretical weight: 1.34 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P43403 (Residues: 286-297; Coverage: 2%)
Gene names: SRK, ZAP70
UbV.pCBL ubiquitin variant Chains: E, F
Molecule details ›
Chains: E, F
Length: 82 amino acids
Theoretical weight: 9.14 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)

Ligands and Environments

2 bound ligands:
Ligand ZN 4 x ZN
Ligand CA 2 x CA
1 modified residue:
Ligand PTR 4 x PTR

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P212121
Unit cell:
a: 94.79Å b: 101.281Å c: 117.339Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.22 0.218 0.248
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

15 review citations

Targeted protein degradation: elements of PROTAC design.
Paiva et al. (2019)
14 more

2 mentions without citation

Emerging drug development technologies targeting ubiquitination for cancer therapeutics.
Veggiani et al. (2019)
1 more