7N2P

AS4.3-RNASEH2b-HLA*B27


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.235 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 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

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F [auth A]
G [auth A]
H [auth A]
I [auth A]
M [auth D]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
M [auth D],
O [auth F]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

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 


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