Solution structure of NDP52 ubiquitin-binding zinc finger

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report

This is version 1.1 of the entry. See complete history


Molecular basis of ubiquitin recognition by the autophagy receptor CALCOCO2

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

(2015) Autophagy 11: 1775-1789

  • DOI: https://doi.org/10.1080/15548627.2015.1082025
  • Primary Citation of Related Structures:  
    2MXP, 4XKL

  • PubMed 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.

  • Organizational Affiliation

    d Unit of Pathogenic Fungal Infection and Host Immunity; Institut Pasteur of Shanghai; Chinese Academy of Science ; Shanghai , China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Calcium-binding and coiled-coil domain-containing protein 233Homo sapiensMutation(s): 0 
Gene Names: CALCOCO2NDP52
UniProt & NIH Common Fund Data Resources
Find proteins for Q13137 (Homo sapiens)
Explore Q13137 
Go to UniProtKB:  Q13137
PHAROS:  Q13137
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13137
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-11
    Type: Initial release
  • Version 1.1: 2023-06-14
    Changes: Data collection, Database references, Derived calculations, Other