2MXP | pdb_00002mxp

Solution structure of NDP52 ubiquitin-binding zinc finger

• PDB DOI: https://doi.org/10.2210/pdb2MXP/pdb
• BMRB: 25423

• Classification: METAL BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-01-12 Released: 2015-11-11 
• Deposition Author(s): Pan, L., Xie, X.

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Experimental Data Snapshot

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

Literature

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

• PubMed: 26506893 
• DOI: https://doi.org/10.1080/15548627.2015.1082025
• Primary Citation 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.

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Organizational Affiliation: 
• a State Key Laboratory of Bioorganic and Natural Products Chemistry.
b Interdisciplinary Research Center on Biology and Chemistry.
d Unit of Pathogenic Fungal Infection and Host Immunity; Institut Pasteur of Shanghai; Chinese Academy of Science ; Shanghai , China.
e Division of Life Science, State Key Laboratory of Molecular Neuroscience; Hong Kong University of Science and Technology ; Kowloon , Hong Kong , China.
c Collaborative Innovation Center of Chemistry for Life Sciences; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences ; Shanghai , China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 3.95 kDa 
• Atom Count: 270 
• Modeled Residue Count: 33 
• Deposited Residue Count: 33 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcium-binding and coiled-coil domain-containing protein 2	A	33	Homo sapiens	Mutation(s): 0  Gene Names: CALCOCO2, NDP52
UniProt & NIH Common Fund Data Resources
Find proteins for Q13137 (Homo sapiens) Explore Q13137  Go to UniProtKB:  Q13137
PHAROS:  Q13137 GTEx:  ENSG00000136436

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-11-11 
Deposition Author(s): Pan, L., Xie, X.

Revision History  

• Version 1.0: 2015-11-11
  Type: Initial release
  
• Version 1.1: 2023-06-14
  Changes: Data collection, Database references, Derived calculations, Other
• Version 1.2: 2024-05-15
  Changes: Data collection, Database references