9NIG | pdb_00009nig

PB TCR in complex with HLA-DR4 presenting citrullinated Tenascin C peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 
    0.260 (Depositor), 0.261 (DCC) 
  • R-Value Work: 
    0.219 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 
    0.221 (Depositor) 

Starting Model: experimental
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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 of 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.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DR alpha chainA,
F [auth C],
K [auth H]
189Homo sapiensMutation(s): 0 
Gene Names: HLA-DRAHLA-DRA1
UniProt & NIH Common Fund Data Resources
Find proteins for P01903 (Homo sapiens)
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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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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen DR beta chainB,
G [auth D],
L [auth I]
190Homo sapiensMutation(s): 0 
Gene Names: HLA-DRB1
UniProt
Find proteins for A0A1V1IGJ9 (Homo sapiens)
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Go to UniProtKB:  A0A1V1IGJ9
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UniProt GroupA0A1V1IGJ9
Glycosylation
Glycosylation Sites: 1
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
PB TCR alpha chainC [auth M],
H [auth E],
M [auth J]
208Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
PB TCR beta chainD [auth N],
I [auth F],
N [auth K]
239Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
TenascinE [auth P],
J [auth G],
O [auth L]
14Homo 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 
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UniProt GroupP24821
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Oligosaccharides

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Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseP [auth O]3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseQ [auth V]2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free:  0.260 (Depositor), 0.261 (DCC) 
  • R-Value Work:  0.219 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 0.221 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.928α = 81.468
b = 88.668β = 76.755
c = 126.07γ = 65.448
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