8OXV

Transglutaminase 3 zymogen in complex with DH patient-derived Fab DH63-B02


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.185 

Starting Models: experimental, in silico
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Autoantibody binding and unique enzyme-substrate intermediate conformation of human transglutaminase 3.

Heggelund, J.E.Das, S.Stamnaes, J.Iversen, R.Sollid, L.M.

(2023) Nat Commun 14: 6216-6216

  • DOI: https://doi.org/10.1038/s41467-023-42004-z
  • Primary Citation of Related Structures:  
    8OXV, 8OXW, 8OXX, 8OXY

  • PubMed Abstract: 

    Transglutaminase 3 (TG3), the autoantigen of dermatitis herpetiformis (DH), is a calcium dependent enzyme that targets glutamine residues in polypeptides for either transamidation or deamidation modifications. To become catalytically active TG3 requires proteolytic cleavage between the core domain and two C-terminal β-barrels (C1C2). Here, we report four X-ray crystal structures representing inactive and active conformations of human TG3 in complex with a TG3-specific Fab fragment of a DH patient derived antibody. We demonstrate that cleaved TG3, upon binding of a substrate-mimicking inhibitor, undergoes a large conformational change as a β-sheet in the catalytic core domain moves and C1C2 detaches. The unique enzyme-substrate conformation of TG3 without C1C2 is recognized by DH autoantibodies. The findings support a model where B-cell receptors of TG3-specific B cells bind and internalize TG3-gluten enzyme-substrate complexes thereby facilitating gluten-antigen presentation, T-cell help and autoantibody production.


  • Organizational Affiliation

    KG Jebsen Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway. j.e.heggelund@medisin.uio.no.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein-glutamine gamma-glutamyltransferase E 27 kDa non-catalytic chain693Homo sapiensMutation(s): 0 
Gene Names: TGM3
EC: 2.3.2.13
UniProt & NIH Common Fund Data Resources
Find proteins for Q08188 (Homo sapiens)
Explore Q08188 
Go to UniProtKB:  Q08188
PHAROS:  Q08188
GTEx:  ENSG00000125780 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08188
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Antibody Fab fragment Heavy chain225Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Antibody Fab fragment light chain216Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.659α = 90
b = 94.04β = 93.463
c = 91.143γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
DIALSdata reduction
PHASERphasing
Cootmodel building
BUCCANEERmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentNorway2020027
Other privateNorwaySKGJ-MED-017
Other governmentNorwayWL-IMMUNOLOGY

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-18
    Type: Initial release