7X9G

Crystal structure of human EDA and EDAR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.249 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural insights into pathogenic mechanism of hypohidrotic ectodermal dysplasia caused by ectodysplasin A variants.

Yu, K.Huang, C.Wan, F.Jiang, C.Chen, J.Li, X.Wang, F.Wu, J.Lei, M.Wu, Y.

(2023) Nat Commun 14: 767-767

  • DOI: https://doi.org/10.1038/s41467-023-36367-6
  • Primary Citation of Related Structures:  
    7X9G

  • PubMed Abstract: 

    EDA is a tumor necrosis factor (TNF) family member, which functions together with its cognate receptor EDAR during ectodermal organ development. Mutations of EDA have long been known to cause X-linked hypohidrotic dysplasia in humans characterized by primary defects in teeth, hair and sweat glands. However, the structural information of EDA interaction with EDAR is lacking and the pathogenic mechanism of EDA variants is poorly understood. Here, we report the crystal structure of EDA C-terminal TNF homology domain bound to the N-terminal cysteine-rich domains of EDAR. Together with biochemical, cellular and mouse genetic studies, we show that different EDA mutations lead to varying degrees of ectodermal developmental defects in mice, which is consistent with the clinical observations on human patients. Our work extends the understanding of the EDA signaling mechanism, and provides important insights into the molecular pathogenesis of disease-causing EDA variants.


  • Organizational Affiliation

    Department of Second Dental Center, Ninth People's Hospital Affiliated with Shanghai Jiao Tong University, School of Medicine, Shanghai Key Laboratory of Stomatology, National Clinical Research Center of Stomatology, Shanghai, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ectodysplasin-A, secreted form
A, B
159Homo sapiensMutation(s): 0 
Gene Names: EDAED1EDA2
UniProt & NIH Common Fund Data Resources
Find proteins for Q92838 (Homo sapiens)
Explore Q92838 
Go to UniProtKB:  Q92838
PHAROS:  Q92838
GTEx:  ENSG00000158813 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92838
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tumor necrosis factor receptor superfamily member EDAR123Homo sapiensMutation(s): 0 
Gene Names: EDARDL
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UNE0 (Homo sapiens)
Explore Q9UNE0 
Go to UniProtKB:  Q9UNE0
PHAROS:  Q9UNE0
GTEx:  ENSG00000135960 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UNE0
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.249 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.169α = 90
b = 87.169β = 90
c = 156.354γ = 120
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing
Cootmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-22
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-11-20
    Changes: Structure summary