5C0B

1E6 TCR in complex with HLA-A02 carrying RQFGPDFPTI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Hotspot autoimmune T cell receptor binding underlies pathogen and insulin peptide cross-reactivity.

Cole, D.K.Bulek, A.M.Dolton, G.Schauenberg, A.J.Szomolay, B.Rittase, W.Trimby, A.Jothikumar, P.Fuller, A.Skowera, A.Rossjohn, J.Zhu, C.Miles, J.J.Peakman, M.Wooldridge, L.Rizkallah, P.J.Sewell, A.K.

(2016) J Clin Invest 126: 2191-2204

  • DOI: 10.1172/JCI85679
  • Primary Citation of Related Structures:  
    5C07, 5C08, 5C09, 5C0A, 5C0B, 5C0C, 5C0D, 5C0E, 5C0F, 5C0G, 5C0I, 5C0J, 5N1Y

  • PubMed Abstract: 
  • The cross-reactivity of T cells with pathogen- and self-derived peptides has been implicated as a pathway involved in the development of autoimmunity. However, the mechanisms that allow the clonal T cell antigen receptor (TCR) to functionally engage multiple peptide-major histocompatibility complexes (pMHC) are unclear ...

    The cross-reactivity of T cells with pathogen- and self-derived peptides has been implicated as a pathway involved in the development of autoimmunity. However, the mechanisms that allow the clonal T cell antigen receptor (TCR) to functionally engage multiple peptide-major histocompatibility complexes (pMHC) are unclear. Here, we studied multiligand discrimination by a human, preproinsulin reactive, MHC class-I-restricted CD8+ T cell clone (1E6) that can recognize over 1 million different peptides. We generated high-resolution structures of the 1E6 TCR bound to 7 altered peptide ligands, including a pathogen-derived peptide that was an order of magnitude more potent than the natural self-peptide. Evaluation of these structures demonstrated that binding was stabilized through a conserved lock-and-key-like minimal binding footprint that enables 1E6 TCR to tolerate vast numbers of substitutions outside of this so-called hotspot. Highly potent antigens of the 1E6 TCR engaged with a strong antipathogen-like binding affinity; this engagement was governed though an energetic switch from an enthalpically to entropically driven interaction compared with the natural autoimmune ligand. Together, these data highlight how T cell cross-reactivity with pathogen-derived antigens might break self-tolerance to induce autoimmune disease.


    Organizational Affiliation

    Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, A-2 alpha chainA, F275Homo sapiensMutation(s): 0 
Gene Names: HLA-AHLAA
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Find proteins for P04439 (Homo sapiens)
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PHAROS:  P04439
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinB, G100Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
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PHAROS:  P61769
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Marker peptideC, H10Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
1E6 TCR Alpha ChainD, I199Homo sapiensMutation(s): 0 
Gene Names: TRACTCRATRAV12-3
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PHAROS:  A0A0B4J271
Find proteins for P01848 (Homo sapiens)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
1E6 TCR Beta ChainE, J247Homo sapiensMutation(s): 0 
Gene Names: TRBV12-4TRBC2TCRBC2
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Find proteins for A0A5B9 (Homo sapiens)
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PHAROS:  A0A5B9
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4

Download Ideal Coordinates CCD File 
BC [auth J]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
CA [auth B], EB [auth F], FB [auth F], GB [auth F], U [auth A], UA [auth E], V [auth A], VA [auth E]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AC [auth J], BA [auth B], DB [auth F], T [auth A], TA [auth E], TB [auth I]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth B] , AB [auth F] , BB [auth F] , CB [auth F] , DA [auth D] , EA [auth D] , FA [auth D] , GA [auth D] , 
AA [auth B], AB [auth F], BB [auth F], CB [auth F], DA [auth D], EA [auth D], FA [auth D], GA [auth D], HA [auth D], HB [auth G], IA [auth D], IB [auth G], JA [auth E], JB [auth G], K [auth A], KA [auth E], KB [auth G], L [auth A], LA [auth E], LB [auth H], M [auth A], MA [auth E], MB [auth I], N [auth A], NA [auth E], NB [auth I], O [auth A], OA [auth E], OB [auth I], P [auth A], PA [auth E], PB [auth I], Q [auth A], QA [auth E], QB [auth I], R [auth A], RA [auth E], RB [auth I], S [auth A], SA [auth E], SB [auth I], UB [auth J], VB [auth J], W [auth B], WA [auth F], WB [auth J], X [auth B], XA [auth F], XB [auth J], Y [auth B], YA [auth F], YB [auth J], Z [auth B], ZA [auth F], ZB [auth J]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.94α = 96.98
b = 100.28β = 98.05
c = 122.44γ = 96.53
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-04
    Type: Initial release
  • Version 1.1: 2016-05-25
    Changes: Database references
  • Version 1.2: 2016-06-08
    Changes: Database references