4XKL

Crystal structure of NDP52 ZF2 in complex with mono-ubiquitin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report



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

  • DOI: 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 targ ...

    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

    c Collaborative Innovation Center of Chemistry for Life Sciences; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences ; Shanghai , China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UbiquitinAC80Homo sapiensMutation(s): 0 
Gene Names: UBA52UBCEP2
Find proteins for P62987 (Homo sapiens)
Explore P62987 
Go to UniProtKB:  P62987
NIH Common Fund Data Resources
PHAROS  P62987
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Calcium-binding and coiled-coil domain-containing protein 2BD33Homo sapiensMutation(s): 0 
Gene Names: CALCOCO2NDP52
Find proteins for Q13137 (Homo sapiens)
Explore Q13137 
Go to UniProtKB:  Q13137
NIH Common Fund Data Resources
PHAROS  Q13137
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.95α = 90
b = 73.8β = 108.49
c = 39.7γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31470749
National Basic Research Program of ChinaChina2013CB836900
China Postdoctoral Science FoundationChina2014M561538

Revision History 

  • Version 1.0: 2015-11-11
    Type: Initial release