5C0C

1E6 TCR in complex with HLA-A02 carrying RQFGPDWIVA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 

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

    Department of Bioscience and Biotechnology Kyushu University Graduate School Fukuoka Japan.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, A-2 alpha chainA, F277Homo sapiensMutation(s): 0 
Gene Names: HLA-AHLAA
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PHAROS:  P04439
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UniProt GroupP04439
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinB, G100Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
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Find proteins for P61769 (Homo sapiens)
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PHAROS:  P61769
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UniProt GroupP61769
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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, I200Homo sapiensMutation(s): 0 
Gene Names: TRAV12-3TRACTCRA
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Find proteins for A0A0B4J271 (Homo sapiens)
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PHAROS:  A0A0B4J271
Find proteins for P01848 (Homo sapiens)
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PHAROS:  P01848
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UniProt GroupsA0A0B4J271P01848
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
1E6 TCR Beta ChainE, J247Homo sapiensMutation(s): 0 
Gene Names: TRBC2TCRBC2TRBV12-4
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Find proteins for A0A5B9 (Homo sapiens)
Explore A0A5B9 
Go to UniProtKB:  A0A5B9
PHAROS:  A0A5B9
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UniProt GroupsA0A5B9A0A0B4J2E0
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Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4

Download Ideal Coordinates CCD File 
N [auth A],
PA [auth I]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
O [auth A],
XA [auth J],
YA [auth J],
ZA [auth J]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
IA [auth F],
JA [auth F],
R [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth E],
BA [auth F],
CA [auth F],
DA [auth F],
EA [auth F],
AA [auth E],
BA [auth F],
CA [auth F],
DA [auth F],
EA [auth F],
FA [auth F],
GA [auth F],
HA [auth F],
K [auth A],
KA [auth G],
L [auth A],
LA [auth G],
M [auth A],
MA [auth I],
NA [auth I],
OA [auth I],
P [auth B],
Q [auth B],
QA [auth J],
RA [auth J],
S [auth D],
SA [auth J],
T [auth D],
TA [auth J],
U [auth D],
UA [auth J],
V [auth E],
VA [auth J],
W [auth E],
WA [auth J],
X [auth E],
Y [auth E],
Z [auth E]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.92α = 96.9
b = 100.37β = 98.02
c = 122.73γ = 96.07
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