› 4a4c

X-ray diffraction
2.7Å resolution

Structure of phosphoTyr371-c-Cbl-UbcH5B-ZAP-70 complex

Released:
DOI: 10.2210/pdb4a4c/pdb
PDB entry 4a4c coloured by chain, front view.
PDB entry 4a4c coloured by chain, side view.
PDB entry 4a4c coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis for autoinhibition and phosphorylation-dependent activation of c-Cbl.
Dou H, Buetow L, Hock A, Sibbet GJ, Vousden KH, Huang DT
Nat Struct Mol Biol 19 184-92 (2012)
PMID: 22266821

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
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
(1a) S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [(E3-independent) E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-monoubiquitinyl-[(E3-independent) ubiquitin-conjugating enzyme]-L-cysteine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-149758 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
E3 ubiquitin-protein ligase CBL Chain: A
Molecule details ›
Chain: A
Length: 391 amino acids
Theoretical weight: 45.15 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 Chain: B
Molecule details ›
Chain: B
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
Ubiquitin-conjugating enzyme E2 D2 Chain: C
Molecule details ›
Chain: C
Length: 147 amino acids
Theoretical weight: 16.76 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P62837 (Residues: 1-147; Coverage: 100%)
Gene names: PUBC1, UBC4, UBC5B, UBCH4, UBCH5B, UBE2D2
Sequence domains: Ubiquitin-conjugating enzyme
Structure domains: Ubiquitin Conjugating Enzyme

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: P6522
Unit cell:
a: 75.285Å b: 75.285Å c: 459.66Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.206 0.203 0.268
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

32 review citations

Ubiquitin Ligases: Structure, Function, and Regulation.
Zheng et al. (2017)
31 more

11 mentions without citation

Macromolecular juggling by ubiquitylation enzymes.
Lorenz et al. (2013)
10 more