› 3zni

X-ray diffraction
2.21Å resolution

Structure of phosphoTyr363-Cbl-b - UbcH5B-Ub - ZAP-70 peptide complex

Released:
DOI: 10.2210/pdb3zni/pdb
PDB entry 3zni coloured by chain, front view.
PDB entry 3zni coloured by chain, side view.
PDB entry 3zni coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Essentiality of a non-RING element in priming donor ubiquitin for catalysis by a monomeric E3.
Dou H, Buetow L, Sibbet GJ, Cameron K, Huang DT
Nat Struct Mol Biol 20 982-986 (2013)
PMID: 23851457

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 tetramer (preferred)
PDBe Complex ID:
PDB-CPX-143348 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
E3 ubiquitin-protein ligase CBL-B Chains: A, E, I, M
Molecule details ›
Chains: A, E, I, M
Length: 394 amino acids
Theoretical weight: 45.75 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q13191 (Residues: 36-427; Coverage: 40%)
Gene names: CBLB, Nbla00127, RNF56
Sequence domains:
Structure domains:
Tyrosine-protein kinase ZAP-70 Chains: B, F, J, N
Molecule details ›
Chains: B, F, J, N
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 Chains: C, G, K, O
Molecule details ›
Chains: C, G, K, O
Length: 146 amino acids
Theoretical weight: 16.72 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P62837 (Residues: 2-147; Coverage: 99%)
Gene names: PUBC1, UBC4, UBC5B, UBCH4, UBCH5B, UBE2D2
Sequence domains: Ubiquitin-conjugating enzyme
Structure domains: Ubiquitin Conjugating Enzyme
Ubiquitin Chains: D, H, L, P
Molecule details ›
Chains: D, H, L, P
Length: 81 amino acids
Theoretical weight: 8.92 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG48 (Residues: 609-684; Coverage: 11%)
Gene name: UBC
Sequence domains: Ubiquitin family
Structure domains: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Ligands and Environments

3 bound ligands:
Ligand ZN 8 x ZN
Ligand CA 4 x CA
Ligand EDO 4 x EDO
1 modified residue:
Ligand PTR 8 x PTR

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04, DIAMOND BEAMLINE I24
Spacegroup: P21
Unit cell:
a: 94.97Å b: 131.8Å c: 122Å
α: 90° β: 91.92° γ: 90°
R-values:
R R work R free
0.177 0.175 0.211
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided
  • Escherichia coli

Quick links

Citations

19 review citations

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

8 mentions without citation

Structural and functional insights to ubiquitin-like protein conjugation.
Streich et al. (2014)
7 more