8TRR

T cell recognition of citrullinated vimentin peptide presented by HLA-DR4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.210 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

The molecular basis underlying T cell specificity towards citrullinated epitopes presented by HLA-DR4.

Loh, T.J.Lim, J.J.Jones, C.M.Dao, H.T.Tran, M.T.Baker, D.G.La Gruta, N.L.Reid, H.H.Rossjohn, J.

(2024) Nat Commun 15: 6201-6201

  • DOI: https://doi.org/10.1038/s41467-024-50511-w
  • Primary Citation of Related Structures:  
    8TRL, 8TRQ, 8TRR

  • PubMed Abstract: 

    CD4 + T cells recognising citrullinated self-epitopes presented by HLA-DRB1 bearing the shared susceptibility epitope (SE) are implicated in rheumatoid arthritis (RA). However, the underlying T cell receptor (TCR) determinants of epitope specificity towards distinct citrullinated peptide antigens, including vimentin-64cit 59-71 and α-enolase-15cit 10-22 remain unclear. Using HLA-DR4-tetramers, we examine the T cell repertoire in HLA-DR4 transgenic mice and observe biased TRAV6 TCR gene usage across these two citrullinated epitopes which matches with TCR bias previously observed towards the fibrinogen β-74cit 69-81 epitope. Moreover, shared TRAV26-1 gene usage is evident in four α-enolase-15cit 10-22 reactive T cells in three human samples. Crystal structures of mouse TRAV6 + and human TRAV26-1 + TCR-HLA-DR4 complexes presenting vimentin-64cit 59-71 and α-enolase-15cit 10-22 , respectively, show three-way interactions between the TCR, SE, citrulline, and the basis for the biased selection of TRAV genes. Position 2 of the citrullinated epitope is a key determinant underpinning TCR specificity. Accordingly, we provide a molecular basis of TCR specificity towards citrullinated epitopes.


  • Organizational Affiliation

    Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Australia.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DR alpha chain
A, F
181Homo 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
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DRB1 beta chain
B, G
190Homo sapiensMutation(s): 17 
Gene Names: HLA-DRB1
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
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P01911-1
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Vimentin
C, H
13Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P08670 (Homo sapiens)
Explore P08670 
Go to UniProtKB:  P08670
PHAROS:  P08670
GTEx:  ENSG00000026025 
Entity Groups  
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UniProt GroupP08670
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
A03 TCR alpha chain
D, I
209Mus musculusMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
A03 TCR beta chain
E, J
243Mus musculusMutation(s): 0 
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  • Reference Sequence
Oligosaccharides

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Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
K, L
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
M
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G47362BJ
GlyCosmos:  G47362BJ
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

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

Download Ideal Coordinates CCD File 
AA [auth E]
EA [auth F]
GA [auth G]
HA [auth G]
IA [auth G]
AA [auth E],
EA [auth F],
GA [auth G],
HA [auth G],
IA [auth G],
JA [auth G],
KA [auth G],
LA [auth I],
MA [auth I],
NA [auth J],
OA [auth J],
Q [auth A],
R [auth A],
V [auth B],
X [auth D],
Z [auth E]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
CA [auth F]
DA [auth F]
FA [auth G]
N [auth A]
O [auth A]
CA [auth F],
DA [auth F],
FA [auth G],
N [auth A],
O [auth A],
P [auth A],
T [auth B],
U [auth B],
W [auth D],
Y [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CIR
Query on CIR
C, H
L-PEPTIDE LINKINGC6 H13 N3 O3ARG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.210 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.929α = 90
b = 59.97β = 90.16
c = 379.159γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia2008981
Janssen PharmaceuticalsUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-31
    Type: Initial release
  • Version 1.1: 2024-08-07
    Changes: Database references
  • Version 1.2: 2024-10-09
    Changes: Structure summary