9NIH | pdb_00009nih

Crystal structure of HLA-DR4 presenting citrullinated Tenascin C peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.219 (Depositor), 0.218 (DCC) 
  • R-Value Work: 
    0.184 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 
    0.186 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

The molecular basis of T cell receptor recognition of citrullinated tenascin-C presented by HLA-DR4.

Dao, H.T.Loh, T.J.Sharma, R.K.Klareskog, L.Malmstrom, V.Reid, H.H.Rossjohn, J.Lim, J.J.

(2025) J Biological Chem 301: 110326-110326

  • DOI: https://doi.org/10.1016/j.jbc.2025.110326
  • Primary Citation Related Structures: 
    9NIG, 9NIH, 9NII

  • PubMed Abstract: 

    CD4 + T cell autoreactivity against citrullinated (cit) self-epitopes presented by HLA-DRB1 is associated with rheumatoid arthritis (RA) pathogenesis. We understand the molecular bases of T cell receptor (TCR) recognition of cit-fibrinogen, cit-vimentin, and cit-α-enolase epitopes, and the role of citrulline in shaping TCR repertoire usage. Nevertheless, how TCRs recognize other cit-epitopes, including tenascin-C (TNC) and how alternative citrullination positions may modulate the T cell recognition remains unclear. Here, we examined TNC 1014,1016cit peptide, which contains citrullination at position P-1 and P2, to study the underlying TCR-HLA-DRB1 04:01-TNC 1014,1016cit molecular interactions. Crystal structure of HLA-DRB1 04:01 TNC1014,1016cit at 2.4 Å resolution revealed a conserved peptide binding register to the established HLA-DRB1 04:01-peptide structures, where both citrullines protruded upward. Next, we determined the crystal structure of a RA patient-derived TRAV35 + /TRBV10-2 + (PB) TCR in complex with HLA-DRB1 04:01 TNC1014,1016cit at 3.2 Å resolution. The CDR3α loop ( 109 VGNTN 113 ) of PB TCR formed a secondary helical conformation at the N-terminus of the peptide binding cleft, allowing extensive interactions between the P-1 and P2 citrullines of TNC 1014,1016cit peptide. Surface plasmon resonance, tetramer staining, and CD69 activation assays revealed that the PB TCR did not cross-react to other RA autoantigens, and the P-1-Cit, P2-Cit, and P5-Tyr of TNC 1014,1016cit are the key determinants underlying the strict specificity of the PB TCR. Collectively, we provide molecular insight into citrullination in modulating TCR recognition.


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

Macromolecule Content 

  • Total Structure Weight: 47.43 kDa 
  • Atom Count: 3,232 
  • Modeled Residue Count: 381 
  • Deposited Residue Count: 401 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DR alpha chain189Homo 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: 1Go to GlyGen: P01903-1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen DR beta chain198Homo sapiensMutation(s): 0 
Gene Names: HLA-DRB1
UniProt
Find proteins for A0A1V1IGJ9 (Homo sapiens)
Explore A0A1V1IGJ9 
Go to UniProtKB:  A0A1V1IGJ9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1V1IGJ9
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Tenascin14Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P24821 (Homo sapiens)
Explore P24821 
Go to UniProtKB:  P24821
PHAROS:  P24821
GTEx:  ENSG00000041982 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24821
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.219 (Depositor), 0.218 (DCC) 
  • R-Value Work:  0.184 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 0.186 (Depositor) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.3α = 90
b = 119.3β = 90
c = 73.273γ = 120
Software Package:
Software NamePurpose
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
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-21
    Type: Initial release
  • Version 1.1: 2025-12-03
    Changes: Database references