5Z7L

Crystal structure of NDP52 SKICH region in complex with NAP1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


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Literature

Mechanistic insights into the interactions of NAP1 with the SKICH domains of NDP52 and TAX1BP1

Fu, T.Liu, J.Wang, Y.Xie, X.Hu, S.Pan, L.

(2018) Proc Natl Acad Sci U S A 115: E11651-E11660

  • DOI: https://doi.org/10.1073/pnas.1811421115
  • Primary Citation of Related Structures:  
    5Z7A, 5Z7G, 5Z7L

  • PubMed Abstract: 

    NDP52 and TAX1BP1, two SKIP carboxyl homology (SKICH) domain-containing autophagy receptors, play crucial roles in selective autophagy. The autophagic functions of NDP52 and TAX1BP1 are regulated by TANK-binding kinase 1 (TBK1), which may associate with them through the adaptor NAP1. However, the molecular mechanism governing the interactions of NAP1 with NDP52 and TAX1BP1, as well as the effects induced by TBK1-mediated phosphorylation of NDP52 and TAX1BP1, remains elusive. Here, we report the atomic structures of the SKICH regions of NDP52 and TAX1BP1 in complex with NAP1, which not only uncover the mechanistic bases underpinning the specific interactions of NAP1 with the SKICH domains of NDP52 and TAX1BP1 but also reveal the binding mode of a SKICH domain. Moreover, we uncovered that the SKICH domains of NDP52 and TAX1BP1 share a general binding mode to interact with NAP1. Finally, we also evaluated the currently known TBK1-mediated phosphorylation sites in the SKICH domains of NDP52 and TAX1BP1 on the basis of their interactions with NAP1. In all, our findings provide mechanistic insights into the interactions of NAP1 with NDP52 and TAX1BP1, and are valuable for further understanding the functions of these proteins in selective autophagy.


  • Organizational Affiliation

    State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 200032 Shanghai, China panlf@sioc.ac.cn.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Calcium-binding and coiled-coil domain-containing protein 2
A, B
117Homo sapiensMutation(s): 0 
Gene Names: CALCOCO2
UniProt & NIH Common Fund Data Resources
Find proteins for Q13137 (Homo sapiens)
Explore Q13137 
Go to UniProtKB:  Q13137
GTEx:  ENSG00000136436 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13137
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
5-azacytidine-induced protein 2
C, D
43Homo sapiensMutation(s): 0 
Gene Names: AZI2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H6S1 (Homo sapiens)
Explore Q9H6S1 
Go to UniProtKB:  Q9H6S1
PHAROS:  Q9H6S1
GTEx:  ENSG00000163512 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H6S1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.173 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.639α = 90
b = 45.026β = 123.77
c = 86.679γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31470749
National Natural Science Foundation of ChinaChina21621002

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-02
    Type: Initial release