8OXX

Transglutaminase 3 in complex with inhibitor Z-don and DH patient-derived Fab DH63-B02


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.154 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 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 chain460Homo 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 chain223Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • 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
Expand
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P6S (Subject of Investigation/LOI)
Query on P6S

Download Ideal Coordinates CCD File 
J [auth A]benzyl hydrogen carbonate
C8 H8 O3
NJAPCAIWQRPQPY-UHFFFAOYSA-N
MLL (Subject of Investigation/LOI)
Query on MLL

Download Ideal Coordinates CCD File 
N [auth A]METHYL L-LEUCINATE
C7 H15 N O2
QVDXUKJJGUSGLS-LURJTMIESA-N
ONL (Subject of Investigation/LOI)
Query on ONL

Download Ideal Coordinates CCD File 
K [auth A]5-OXO-L-NORLEUCINE
C6 H11 N O3
KSIJECNNZVKMJG-YFKPBYRVSA-N
DVA (Subject of Investigation/LOI)
Query on DVA

Download Ideal Coordinates CCD File 
L [auth A]D-VALINE
C5 H11 N O2
KZSNJWFQEVHDMF-SCSAIBSYSA-N
DPR (Subject of Investigation/LOI)
Query on DPR

Download Ideal Coordinates CCD File 
M [auth A]D-PROLINE
C5 H9 N O2
ONIBWKKTOPOVIA-SCSAIBSYSA-N
SO4
Query on SO4

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D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

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E [auth A]
F [auth A]
O [auth B]
P [auth B]
Q [auth C]
E [auth A],
F [auth A],
O [auth B],
P [auth B],
Q [auth C],
R [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
I [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.271α = 90
b = 65.005β = 96.854
c = 90.908γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
REFMACrefinement
Cootmodel building
PHASERphasing
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection