5C08

1E6 TCR in Complex with HLA-A0e carrying RQWGPDPAAV


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.209 

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:  
    5C0A, 5C07, 5C09, 5C08, 5C0J, 5C0C, 5C0B, 5C0E, 5C0D, 5C0G

  • 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 ...

    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

    Molecular & Structural Biology Division, Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, U.P., India. Electronic address: r_ravishankar@cdri.res.in.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, A-2 alpha chainAF276Homo sapiensMutation(s): 0 
Gene Names: HLA-AHLAA
Find proteins for P04439 (Homo sapiens)
Explore P04439 
Go to UniProtKB:  P04439
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PHAROS  P04439
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinBG100Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
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PHAROS  P61769
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Marker peptideCH10Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
1E6 TCR Alpha ChainDI191Homo sapiensMutation(s): 0 
Gene Names: TRACTCRATRAV12-3
Find proteins for A0A0B4J271 (Homo sapiens)
Explore A0A0B4J271 
Go to UniProtKB:  A0A0B4J271
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PHAROS  A0A0B4J271
Find proteins for P01848 (Homo sapiens)
Explore P01848 
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PHAROS  P01848
Protein Feature View
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
1E6 TCR Beta ChainEJ245Homo sapiensMutation(s): 0 
Gene Names: TRBV12-4TRBC2TCRBC2
Find proteins for A0A0B4J2E0 (Homo sapiens)
Explore A0A0B4J2E0 
Go to UniProtKB:  A0A0B4J2E0
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Find proteins for A0A5B9 (Homo sapiens)
Explore A0A5B9 
Go to UniProtKB:  A0A5B9
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PHAROS  A0A5B9
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
D, E, F, J
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A, D, E
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A, B, C, D, E, F, G, I, J
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.209 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.8α = 96.33
b = 99.26β = 98.07
c = 122.15γ = 96.42
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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