5V4M | pdb_00005v4m

Structure of HLA-DR15 with bound alpha3(135-145) peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.244 (Depositor), 0.244 (DCC) 
  • R-Value Work: 
    0.217 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 
    0.217 (Depositor) 

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This is version 2.1 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: https://doi.org/10.1038/nature22329
  • Primary Citation Related Structures: 
    5V4M, 5V4N

  • 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 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 (α3 135-145 ). 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 α3 135-145 -specific T cells expand in patients with Goodpasture disease and, in α3 135-145 -immunized HLA-DR15 transgenic mice, α3 135-145 -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 α3 135-145 epitope in different binding registers. HLA-DR15-α3 135-145 tetramer + T cells in HLA-DR15 transgenic mice exhibit a conventional T-cell phenotype (T conv ) that secretes pro-inflammatory cytokines. In contrast, HLA-DR1-α3 135-145 tetramer + T cells in HLA-DR1 and HLA-DR15/DR1 transgenic mice are predominantly CD4 + Foxp3 + regulatory T cells (T reg cells) expressing tolerogenic cytokines. HLA-DR1-induced T reg cells confer resistance to disease in HLA-DR15/DR1 transgenic mice. HLA-DR15 + and HLA-DR1 + healthy human donors display altered α3 135-145 -specific T-cell antigen receptor usage, HLA-DR15-α3 135-145 tetramer + Foxp3 - T conv and HLA-DR1-α3 135-145 tetramer + Foxp3 + CD25 hi CD127 lo T reg dominant phenotypes. Moreover, patients with Goodpasture disease display a clonally expanded α3 135-145 -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 T reg 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.

Macromolecule Content 

  • Total Structure Weight: 189.02 kDa 
  • Atom Count: 13,349 
  • Modeled Residue Count: 1,512 
  • Deposited Residue Count: 1,620 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HLA-DRA1A [auth D],
C [auth A],
E [auth G],
G [auth J]
189Homo sapiensMutation(s): 0 
Gene Names: HLA-DRAHLA-DRA1
UniProt & NIH Common Fund Data Resources
Find proteins for P01903 (Homo sapiens)
Explore P01903 
Go to UniProtKB:  P01903
PHAROS:  P01903
GTEx:  ENSG00000204287 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01903
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P01903-1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
alpha3(135-145)-HLA-DRB1*15:01B [auth F],
D [auth C],
F [auth I],
H [auth L]
216Homo sapiensMutation(s): 0 
Gene Names: HLA-DRB1HLA-DRB2
UniProt & NIH Common Fund Data Resources
Find proteins for P01911 (Homo sapiens)
Explore P01911 
Go to UniProtKB:  P01911
PHAROS:  P01911
GTEx:  ENSG00000196126 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01911
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-L-fucopyranose-(1-3)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseI [auth B],
K [auth H]
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G04836KE
GlyCosmos: G04836KE
GlyGen: G04836KE
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseJ [auth E],
L [auth K]
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.244 (Depositor), 0.244 (DCC) 
  • R-Value Work:  0.217 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 0.217 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.59α = 87.64
b = 79.01β = 73.29
c = 95.821γ = 89.97
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-03
    Type: Initial release
  • Version 1.1: 2017-05-17
    Changes: Database references
  • Version 1.2: 2017-05-24
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-10-09
    Changes: Data collection, Database references, Derived calculations, Structure summary