8BBH | pdb_00008bbh

The crystal structure of a mouse Fab fragment TL1 in complex with a human Glucose-6-phosphate isomerase peptide 293-307


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 
    0.229 (Depositor), 0.229 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.198 (DCC) 

Starting Model: other
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wwPDB Validation 3D Report Full Report

Validation slider image for 8BBH

This is version 1.3 of the entry. See complete history

Literature

Pathogenic antibody response to glucose-6-phosphate isomerase targets a modified epitope uniquely exposed on joint cartilage.

Li, T.Ge, C.Kramer, A.Sareila, O.Leu Agelii, M.Johansson, L.Forslind, K.Lonnblom, E.Yang, M.Xu, B.Li, Q.Cheng, L.Bergstrom, G.Fernandez, G.Kastbom, A.Rantapaa-Dahlqvist, S.Gjertsson, I.Holmdahl, R.

(2023) Ann Rheum Dis 82: 799-808

  • DOI: https://doi.org/10.1136/ard-2022-223633
  • Primary Citation Related Structures: 
    8BBH

  • PubMed Abstract: 

    To identify the arthritogenic B cell epitopes of glucose-6-phosphate isomerase (GPI) and their association with rheumatoid arthritis (RA). IgG response towards a library of GPI peptides in patients with early RA, pre-symptomatic individuals and population controls, as well as in mice, were tested by bead-based multiplex immunoassays and ELISA. Monoclonal IgG were generated, and the binding specificity and affinity were determined by ELISA, gel size exclusion chromatography, surface plasma resonance and X-ray crystallography. Arthritogenicity was investigated by passive transfer experiments. Antigen-specific B cells were identified by peptide tetramer staining. Peptide GPI 293-307 was the dominant B cell epitope in K/BxN and GPI-immunised mice. We could detect B cells and low levels of IgM antibodies binding the GPI 293-307 epitopes, and high affinity anti-GPI 293-307 IgG antibodies already 7 days after GPI immunisation, immediately before arthritis onset. Transfer of anti-GPI 293-307 IgG antibodies induced arthritis in mice. Moreover, anti-GPI 293-307 IgG antibodies were more frequent in individuals prior to RA onset (19%) than in controls (7.5%). GPI 293-307 -specific antibodies were associated with radiographic joint damage. Crystal structures of the Fab-peptide complex revealed that this epitope is not exposed in native GPI but requires conformational change of the protein in inflamed joint for effective recognition by anti-GPI 293-307 antibodies. We have identified the major pathogenic B cell epitope of the RA-associated autoantigen GPI, at position 293-307, exposed only on structurally modified GPI on the cartilage surface. B cells to this neo-epitope escape tolerance and could potentially play a role in the pathogenesis of RA.


  • Organizational Affiliation
    • Section of Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden.

Macromolecule Content 

  • Total Structure Weight: 48.74 kDa 
  • Atom Count: 3,681 
  • Modeled Residue Count: 439 
  • Deposited Residue Count: 450 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glucose-6-phosphate isomerase19Homo sapiensMutation(s): 0 
EC: 5.3.1.9 (PDB Primary Data), 5.1.3 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P06744 (Homo sapiens)
Explore P06744 
Go to UniProtKB:  P06744
PHAROS:  P06744
GTEx:  ENSG00000105220 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06744
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Heavy Chain of TL1 Fab fragmentB [auth H]213Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Light Chain of TL1 Fab fragmentC [auth L]218Mus musculusMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free:  0.229 (Depositor), 0.229 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.198 (DCC) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.66α = 90
b = 75.545β = 90
c = 96.219γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Knut and Alice Wallenberg FoundationSwedenKAW 2019.0059
Swedish Research CouncilSweden2019-01209

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-21
    Type: Initial release
  • Version 1.1: 2023-07-05
    Changes: Database references, Structure summary
  • Version 1.2: 2024-10-23
    Changes: Data collection, Structure summary
  • Version 1.3: 2026-03-04
    Changes: Refinement description