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), 0.246 (DCC) 
  • R-Value Work: 
    0.230 (Depositor) 
  • R-Value Observed: 
    0.235 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


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 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.

Macromolecule Content 

  • Total Structure Weight: 96.17 kDa 
  • Atom Count: 6,623 
  • Modeled Residue Count: 809 
  • Deposited Residue Count: 833 
  • Unique protein chains: 5

Macromolecules

Find similar proteins by:|  3D Structure
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
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61769
Sequence Annotations
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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
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
AS4.3 T cell receptor alpha chain204Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
AS4.3 T cell receptor beta chainE [auth F]242Homo sapiensMutation(s): 0 

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]
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

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.288 (Depositor), 0.246 (DCC) 
  • R-Value Work:  0.230 (Depositor) 
  • 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 


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