PDBsum entry 4xkl

Protein binding/metal binding protein

PDB id: 4xkl

Contents

Protein chains

78 a.a.

30 a.a.

31 a.a.

Ligands

GOL ×2

ACT ×4

Metals

_ZN ×2

Waters ×106

PDB id:

4xkl

Name:

Protein binding/metal binding protein

Title:

Crystal structure of ndp52 zf2 in complex with mono-ubiquitin

Structure:

Ubiquitin. Chain: a, c. Engineered: yes. Calcium-binding and coiled-coil domain-containing protein 2. Chain: b, d. Fragment: zinc finger, unp residues 414-446. Synonym: antigen nuclear dot 52 kda protein,nuclear domain 10 protein ndp52,nuclear domain 10 protein 52,nuclear dot protein 52.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: uba52. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: calcoco2, ndp52.

Resolution:

2.10Å R-factor: 0.196 R-free: 0.243

Authors:

X.Xie,F.Li,Y.Wang,Z.Lin,X.Chen,J.Liu,L.Pan

Key ref:

X.Xie et al. (2015). Molecular basis of ubiquitin recognition by the autophagy receptor CALCOCO2. Autophagy, 11, 1775-1789. PubMed id: 26506893 DOI: 10.1080/15548627.2015.1082025

Date:

12-Jan-15 Release date: 11-Nov-15

Protein chains

P62987  (RL40_HUMAN) -  Ubiquitin-ribosomal protein eL40 fusion protein from Homo sapiens

Seq: 128 a.a.

Struc: 78 a.a.

Protein chain

Q13137  (CACO2_HUMAN) -  Calcium-binding and coiled-coil domain-containing protein 2 from Homo sapiens

Seq: 446 a.a.

Struc: 30 a.a.

Protein chain

Q13137  (CACO2_HUMAN) -  Calcium-binding and coiled-coil domain-containing protein 2 from Homo sapiens

Seq: 446 a.a.

Struc: 31 a.a.

DOI no: 10.1080/15548627.2015.1082025

Autophagy 11:1775-1789 (2015)

PubMed id: 26506893

Molecular basis of ubiquitin recognition by the autophagy receptor CALCOCO2.

X.Xie, F.Li, Y.Wang, Y.Wang, Z.Lin, X.Cheng, J.Liu, C.Chen, L.Pan.

ABSTRACT

The autophagy receptor CALCOCO2/NDP52 functions as a bridging adaptor and plays an essential role in the selective autophagic degradation of invading pathogens by specifically recognizing ubiquitin-coated intracellular pathogens and subsequently targeting them to the autophagic machinery; thereby it is required for innate immune defense against a range of infectious pathogens in mammals. However, the mechanistic basis underlying CALCOCO2-mediated specific recognition of ubiqutinated pathogens is still unknown. Here, using biochemical and structural analyses, we demonstrated that the cargo-binding region of CALCOCO2 contains a dynamic unconventional zinc finger as well as a C2H2-type zinc-finger, and only the C2H2-type zinc finger specifically recognizes mono-ubiquitin or poly-ubiquitin chains. In addition to elucidating the specific ubiquitin recognition mechanism of CALCOCO2, the structure of the CALCOCO2 C2H2-type zinc finger in complex with mono-ubiquitin also uncovers a unique zinc finger-binding mode for ubiquitin. Our findings provide mechanistic insight into how CALCOCO2 targets ubiquitin-decorated pathogens for autophagic degradations.