5V4N

Structure of HLA-DR1 with bound alpha3(135-145) peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.405 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Dominant protection from HLA-linked autoimmunity by antigen-specific regulatory T cells.

Ooi, J.D.Petersen, J.Tan, Y.H.Huynh, M.Willett, Z.J.Ramarathinam, S.H.Eggenhuizen, P.J.Loh, K.L.Watson, K.A.Gan, P.Y.Alikhan, M.A.Dudek, N.L.Handel, A.Hudson, B.G.Fugger, L.Power, D.A.Holt, S.G.Coates, P.T.Gregersen, J.W.Purcell, A.W.Holdsworth, S.R.La Gruta, N.L.Reid, H.H.Rossjohn, J.Kitching, A.R.

(2017) Nature 545: 243-247

  • DOI: 10.1038/nature22329
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Susceptibility and protection against human autoimmune diseases, including type I diabetes, multiple sclerosis, and Goodpasture disease, is associated with particular human leukocyte antigen (HLA) alleles. However, the mechanisms underpinning such HL ...

    Susceptibility and protection against human autoimmune diseases, including type I diabetes, multiple sclerosis, and Goodpasture disease, is associated with particular human leukocyte antigen (HLA) alleles. However, the mechanisms underpinning such HLA-mediated effects on self-tolerance remain unclear. Here we investigate the molecular mechanism of Goodpasture disease, an HLA-linked autoimmune renal disorder characterized by an immunodominant CD4+ T-cell self-epitope derived from the α3 chain of type IV collagen (α3135-145). While HLA-DR15 confers a markedly increased disease risk, the protective HLA-DR1 allele is dominantly protective in trans with HLA-DR15 (ref. 2). We show that autoreactive α3135-145-specific T cells expand in patients with Goodpasture disease and, in α3135-145-immunized HLA-DR15 transgenic mice, α3135-145-specific T cells infiltrate the kidney and mice develop Goodpasture disease. HLA-DR15 and HLA-DR1 exhibit distinct peptide repertoires and binding preferences and present the α3135-145 epitope in different binding registers. HLA-DR15-α3135-145 tetramer+ T cells in HLA-DR15 transgenic mice exhibit a conventional T-cell phenotype (Tconv) that secretes pro-inflammatory cytokines. In contrast, HLA-DR1-α3135-145 tetramer+ T cells in HLA-DR1 and HLA-DR15/DR1 transgenic mice are predominantly CD4+Foxp3+ regulatory T cells (Treg cells) expressing tolerogenic cytokines. HLA-DR1-induced Treg cells confer resistance to disease in HLA-DR15/DR1 transgenic mice. HLA-DR15+ and HLA-DR1+ healthy human donors display altered α3135-145-specific T-cell antigen receptor usage, HLA-DR15-α3135-145 tetramer+ Foxp3- Tconv and HLA-DR1-α3135-145 tetramer+ Foxp3+CD25hiCD127lo Treg dominant phenotypes. Moreover, patients with Goodpasture disease display a clonally expanded α3135-145-specific CD4+ T-cell repertoire. Accordingly, we provide a mechanistic basis for the dominantly protective effect of HLA in autoimmune disease, whereby HLA polymorphism shapes the relative abundance of self-epitope specific Treg cells that leads to protection or causation of autoimmunity.


    Organizational Affiliation

    Centre for Inflammatory Diseases, Monash University Department of Medicine, Monash Medical Centre, Clayton, Victoria 3168, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA-DRA1
A, D
189Homo sapiensMutation(s): 0 
Gene Names: HLA-DRA (HLA-DRA1)
Find proteins for P01903 (Homo sapiens)
Go to Gene View: HLA-DRA
Go to UniProtKB:  P01903
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
alpha3(135-145)-HLA-DRB1*01:01
C, F
216Homo sapiensMutation(s): 0 
Gene Names: HLA-DRB1
Find proteins for P04229 (Homo sapiens)
Go to Gene View: HLA-DRB1
Go to UniProtKB:  P04229
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, D, F
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.405 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 82.086α = 90.00
b = 118.410β = 90.00
c = 120.875γ = 90.00
Software Package:
Software NamePurpose
iMOSFLMdata reduction
PHENIXrefinement
PHASERphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-05-03
    Type: Initial release
  • Version 1.1: 2017-05-17
    Type: Database references
  • Version 1.2: 2017-05-24
    Type: Database references