4XKL | pdb_00004xkl

Crystal structure of NDP52 ZF2 in complex with mono-ubiquitin

• PDB DOI: https://doi.org/10.2210/pdb4XKL/pdb

• Classification: PROTEIN BINDING/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): Xie, X., Li, F., Wang, Y., Lin, Z., Chen, X., Liu, J., Pan, L.
• Funding Organization(s): National Natural Science Foundation of China, National Basic Research Program of China, China Postdoctoral Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.243 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

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: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 26.08 kDa 
• Atom Count: 1,894 
• Modeled Residue Count: 217 
• Deposited Residue Count: 226 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	A, C	80	Homo sapiens	Mutation(s): 0  Gene Names: UBA52
UniProt & NIH Common Fund Data Resources
Find proteins for P62987 (Homo sapiens) Explore P62987  Go to UniProtKB:  P62987
PHAROS:  P62987 GTEx:  ENSG00000221983

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcium-binding and coiled-coil domain-containing protein 2	B, D	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A], I [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	H [auth B], L [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	F [auth B], G [auth B], J [auth C], K [auth D]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.243 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.95	α = 90
b = 73.8	β = 108.49
c = 39.7	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-11-11 
Deposition Author(s): Xie, X., Li, F., Wang, Y., Lin, Z., Chen, X., Liu, J., Pan, L.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31470749
National Basic Research Program of China	China	2013CB836900
China Postdoctoral Science Foundation	China	2014M561538

Revision History  

• Version 1.0: 2015-11-11
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-10-30
  Changes: Structure summary