8TRL

T cell recognition of citrullinated alpha-enolase peptide presented by HLA-DR4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 

Starting Model: experimental
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This is version 2.1 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 chainA,
F [auth D]
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 chainB,
G [auth E]
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
Alpha-enolaseC,
H [auth F]
13Homo sapiensMutation(s): 0 
EC: 4.2.1.11
UniProt & NIH Common Fund Data Resources
Find proteins for P06733 (Homo sapiens)
Explore P06733 
Go to UniProtKB:  P06733
PHAROS:  P06733
GTEx:  ENSG00000074800 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06733
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
RA2.7 TCR alpha chainD [auth I],
I [auth G]
204Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
RA2.7 TCR beta chainE [auth J],
J [auth H]
245Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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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
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)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
L
6N-Glycosylation
Glycosylation Resources
GlyTouCan:  G94156YI
GlyCosmos:  G94156YI
GlyGen:  G94156YI
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
M [auth A],
S [auth B],
V [auth D],
Z [auth E]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL
Query on GOL

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AA [auth E]
BA [auth E]
CA [auth E]
DA [auth E]
EA [auth E]
AA [auth E],
BA [auth E],
CA [auth E],
DA [auth E],
EA [auth E],
FA [auth G],
GA [auth G],
R [auth A],
T [auth B],
X [auth D],
Y [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT
Query on ACT

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HA [auth H],
N [auth A],
Q [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
FMT
Query on FMT

Download Ideal Coordinates CCD File 
O [auth A],
P [auth A],
U [auth J],
W [auth D]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CIR
Query on CIR
C,
H [auth F]
L-PEPTIDE LINKINGC6 H13 N3 O3ARG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 185.857α = 90
b = 58.546β = 113.6
c = 216.479γ = 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 2.0: 2024-09-11
    Changes: Atomic model, Data collection
  • Version 2.1: 2024-11-13
    Changes: Structure summary