7N2P | pdb_00007n2p

AS4.3-RNASEH2b-HLA*B27


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.288 (Depositor), 0.290 (DCC) 
  • R-Value Work: 
    0.230 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.235 (Depositor) 

Starting Models: experimental
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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view details

This is version 1.5 of the entry. See complete history


Literature

Autoimmunity-associated T cell receptors recognize HLA-B*27-bound peptides.

Yang, X.Garner, L.I.Zvyagin, I.V.Paley, M.A.Komech, E.A.Jude, K.M.Zhao, X.Fernandes, R.A.Hassman, L.M.Paley, G.L.Savvides, C.S.Brackenridge, S.Quastel, M.N.Chudakov, D.M.Bowness, P.Yokoyama, W.M.McMichael, A.J.Gillespie, G.M.Garcia, K.C.

(2022) Nature 612: 771-777

  • DOI: https://doi.org/10.1038/s41586-022-05501-7
  • Primary Citation of Related Structures:  
    7N2N, 7N2O, 7N2P, 7N2Q, 7N2R, 7N2S, 8CX4

  • PubMed Abstract: 

    Human leucocyte antigen B*27 (HLA-B*27) is strongly associated with inflammatory diseases of the spine and pelvis (for example, ankylosing spondylitis (AS)) and the eye (that is, acute anterior uveitis (AAU)) 1 . How HLA-B*27 facilitates disease remains unknown, but one possible mechanism could involve presentation of pathogenic peptides to CD8 + T cells. Here we isolated orphan T cell receptors (TCRs) expressing a disease-associated public β-chain variable region-complementary-determining region 3β (BV9-CDR3β) motif 2-4 from blood and synovial fluid T cells from individuals with AS and from the eye in individuals with AAU. These TCRs showed consistent α-chain variable region (AV21) chain pairing and were clonally expanded in the joint and eye. We used HLA-B*27:05 yeast display peptide libraries to identify shared self-peptides and microbial peptides that activated the AS- and AAU-derived TCRs. Structural analysis revealed that TCR cross-reactivity for peptide-MHC was rooted in a shared binding motif present in both self-antigens and microbial antigens that engages the BV9-CDR3β TCRs. These findings support the hypothesis that microbial antigens and self-antigens could play a pathogenic role in HLA-B*27-associated disease.


  • Organizational Affiliation

    Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Human leukocyte antigen (HLA) B27278Homo sapiensMutation(s): 1 
UniProt
Find proteins for A3F718 (Homo sapiens)
Explore A3F718 
Go to UniProtKB:  A3F718
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UniProt GroupA3F718
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin100Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
PHAROS:  P61769
GTEx:  ENSG00000166710 
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UniProt GroupP61769
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonuclease H2 subunit B9Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for A0A2R8Y7R8 (Homo sapiens)
Explore A0A2R8Y7R8 
Go to UniProtKB:  A0A2R8Y7R8
GTEx:  ENSG00000136104 
Entity Groups  
UniProt GroupA0A2R8Y7R8
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
AS4.3 T cell receptor alpha chain204Homo sapiensMutation(s): 0 
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Glycosylation
Glycosylation Sites: 3
Sequence Annotations
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
AS4.3 T cell receptor beta chainE [auth F]242Homo sapiensMutation(s): 0 
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Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
J [auth D],
K [auth D],
L [auth D],
N [auth F]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
P [auth F]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
M [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.288 (Depositor), 0.290 (DCC) 
  • R-Value Work:  0.230 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.235 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.925α = 90
b = 93.992β = 90
c = 177.774γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States5R01AI103867

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-07
    Type: Initial release
  • Version 1.1: 2022-12-21
    Changes: Database references
  • Version 1.2: 2023-01-04
    Changes: Database references
  • Version 1.3: 2023-02-15
    Changes: Data collection
  • Version 1.4: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.5: 2024-10-23
    Changes: Structure summary