8RMY | pdb_00008rmy

Transglutaminase 3 in complex with inhibitor Z-don and DH patient-derived Fab DH63-A02


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 
    0.242 (Depositor), 0.248 (DCC) 
  • R-Value Work: 
    0.195 (Depositor), 0.203 (DCC) 

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

Validation slider image for 8RMY

This is version 1.1 of the entry. See complete history

Literature

Enzyme-activating B-cell receptors boost antigen presentation to pathogenic T cells in gluten-sensitive autoimmunity.

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

(2025) Nat Commun 16: 2387-2387

  • DOI: https://doi.org/10.1038/s41467-025-57564-5
  • Primary Citation Related Structures: 
    8RMX, 8RMY

  • PubMed Abstract: 

    Autoantibodies against the enzyme transglutaminase 3 (TG3) are characteristic to the gluten-sensitive skin disorder dermatitis herpetiformis (DH), which is an extraintestinal manifestation of celiac disease. We here demonstrate that TG3-specific B cells can activate gluten-specific CD4 + T cells through B-cell receptor (BCR)-mediated internalization of TG3-gluten enzyme-substrate complexes. Stereotypic anti-TG3 antibodies using IGHV2-5/IGKV4-1 gene segments enhance the catalytic activity of TG3, and this effect translates into increased gluten presentation to T cells when such antibodies are expressed as BCRs. The crystal structure of TG3 bound to an IGHV2-5/IGKV4-1 Fab shows that antibody binding to a β-sheet in the catalytic core domain causes the enzyme to adopt the active conformation. This mechanism explains the production of stereotypic anti-TG3 autoantibodies in DH and highlights a role for TG3-specific B cells as antigen-presenting cells for gluten-specific T cells. Similar boosting effects of autoreactive BCRs could be relevant for other autoimmune diseases, including rheumatoid arthritis.


  • Organizational Affiliation
    • Norwegian Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway. rasmus.iversen@medisin.uio.no.

Macromolecule Content 

  • Total Structure Weight: 200.35 kDa 
  • Atom Count: 13,890 
  • Modeled Residue Count: 1,783 
  • Deposited Residue Count: 1,818 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Antibody Fab fragment light chain IGKV4-1A [auth F],
B [auth C]
219Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein-glutamine gamma-glutamyltransferase EC [auth A],
D
464Homo 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
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Antibody Fab fragment heavy chain IGHV2-5E,
F [auth B]
221Homo sapiensMutation(s): 0 
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
P6S-ONL-VAL-PRO-MLLG [auth J],
H [auth K]
5synthetic constructMutation(s): 0 

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FLC

Query on FLC



Download:Ideal Coordinates CCD File
I [auth A],
O [auth D]
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
PO4

Query on PO4



Download:Ideal Coordinates CCD File
N [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO

Query on EDO



Download:Ideal Coordinates CCD File
J [auth A],
S [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA
(Subject of Investigation/LOI)

Query on CA



Download:Ideal Coordinates CCD File
K [auth A]
L [auth A]
M [auth A]
P [auth D]
Q [auth D]
K [auth A],
L [auth A],
M [auth A],
P [auth D],
Q [auth D],
R [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MLL
Query on MLL
G [auth J],
H [auth K]
L-PEPTIDE LINKINGC7 H15 N O2LEU
ONL
Query on ONL
G [auth J],
H [auth K]
L-PEPTIDE LINKINGC6 H11 N O3

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.242 (Depositor), 0.248 (DCC) 
  • R-Value Work:  0.195 (Depositor), 0.203 (DCC) 
Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.184α = 90
b = 260.191β = 95.1
c = 139.024γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentNorwaysouth eastern norway regional health authority (project 2020027)
Other privateNorwayStiftelsen KG Jebsen (project SKGJ-MED-017)
Other governmentNorwayUniversity of Oslo World-leading research program on human immunology (WL-IMMUNOLOGY).

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-12
    Type: Initial release
  • Version 1.1: 2025-03-19
    Changes: Database references