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 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.154 (Depositor), 0.160 (DCC) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted P6SClick on this verticalbar to view detailsBest fitted MLLClick on this verticalbar to view detailsBest fitted ONLClick on this verticalbar to view detailsBest fitted DVAClick on this verticalbar to view detailsBest fitted DPRClick on this verticalbar to view details

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

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.222 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.154 (Depositor), 0.160 (DCC) 
Space Group: P 1 21 1
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

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted P6SClick on this verticalbar to view detailsBest fitted MLLClick on this verticalbar to view detailsBest fitted ONLClick on this verticalbar to view detailsBest fitted DVAClick on this verticalbar to view detailsBest fitted DPRClick on this verticalbar to view details

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