› 4xib

X-ray diffraction
2.15Å resolution

Crystal structure of the MZM-REP domains of Mind bomb 1 in complex with fly Delta N-box peptide

Released:
DOI: 10.2210/pdb4xib/pdb
PDB entry 4xib coloured by chain, front view.
PDB entry 4xib coloured by chain, side view.
PDB entry 4xib coloured by chain, top view.
Source organisms:
Primary publication:
A tail of two sites: a bipartite mechanism for recognition of notch ligands by mind bomb E3 ligases.
McMillan BJ, Schnute B, Ohlenhard N, Zimmerman B, Miles L, Beglova N, Klein T, Blacklow SC
Mol Cell 57 912-924 (2015)
PMID: 25747658

Function and Biology Details

Reaction 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
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-145150 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
E3 ubiquitin-protein ligase MIB1 Chain: A
Molecule details ›
Chain: A
Length: 380 amino acids
Theoretical weight: 42.15 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q86YT6 (Residues: 8-402; Coverage: 38%)
Gene names: DIP1, KIAA1323, MIB1, ZZANK2
Sequence domains:
Neurogenic locus protein delta Chain: C
Molecule details ›
Chain: C
Length: 11 amino acids
Theoretical weight: 1.32 KDa
Source organism: Drosophila melanogaster
Expression system: Not provided
UniProt:
  • Canonical: P10041 (Residues: 680-690; Coverage: 1%)
Gene names: CG3619, Delta, Dl

Ligands and Environments

2 bound ligands:
Ligand ZN 2 x ZN
Ligand SO4 2 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: P4122
Unit cell:
a: 74.131Å b: 74.131Å c: 170.174Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.212 0.209 0.244
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

9 review citations

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

1 mention without citation

A tail of two sites: a bipartite mechanism for recognition of notch ligands by mind bomb E3 ligases.
McMillan et al. (2015)