› 5z7l

X-ray diffraction
2.02Å resolution

Crystal structure of NDP52 SKICH region in complex with NAP1

Released:
DOI: 10.2210/pdb5z7l/pdb
PDB entry 5z7l coloured by chain, front view.
PDB entry 5z7l coloured by chain, side view.
PDB entry 5z7l coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Mechanistic insights into the interactions of NAP1 with the SKICH domains of NDP52 and TAX1BP1.
Fu T, Liu J, Wang Y, Xie X, Hu S, Pan L
Proc Natl Acad Sci U S A 115 E11651-E11660 (2018)
PMID: 30459273

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-171555 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Calcium-binding and coiled-coil domain-containing protein 2 Chains: A, B
Molecule details ›
Chains: A, B
Length: 117 amino acids
Theoretical weight: 14.02 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli-Pichia pastoris shuttle vector pPpARG4
UniProt:
  • Canonical: Q13137 (Residues: 10-126; Coverage: 26%)
Gene names: CALCOCO2, NDP52
Sequence domains: SKICH domain
Structure domains: Immunoglobulin-like
5-azacytidine-induced protein 2 Chains: C, D
Molecule details ›
Chains: C, D
Length: 43 amino acids
Theoretical weight: 5.06 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli-Pichia pastoris shuttle vector pPpARG4
UniProt:
  • Canonical: Q9H6S1 (Residues: 33-75; Coverage: 11%)
Gene names: AZI2, NAP1, TBKBP2

Ligands and Environments

1 bound ligand:
Ligand GOL 4 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U1
Spacegroup: C2
Unit cell:
a: 113.639Å b: 45.026Å c: 86.679Å
α: 90° β: 123.77° γ: 90°
R-values:
R R work R free
0.173 0.17 0.222
Expression system: Escherichia coli-Pichia pastoris shuttle vector pPpARG4

Quick links

Citations

4 review citations

The exploitation of host autophagy and ubiquitin machinery by Mycobacterium tuberculosis in shaping immune responses and host defense during infection.
Shariq et al. (2023)
3 more

4 mentions without citation

Mechanisms underlying ubiquitin-driven selective mitochondrial and bacterial autophagy.
Goodall et al. (2022)
3 more