7Z50

Structure of the highly diabetogenic 4.1-T cell receptor targeting a hybrid insulin peptide bound to I-Ag7.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Structural plasticity in I-A g7 links autoreactivity to hybrid insulin peptides in type I diabetes.

Erausquin, E.Serra, P.Parras, D.Santamaria, P.Lopez-Sagaseta, J.

(2022) Front Immunol 13: 924311-924311

  • DOI: https://doi.org/10.3389/fimmu.2022.924311
  • Primary Citation of Related Structures:  
    7QHP, 7Z50

  • PubMed Abstract: 

    We recently provided evidence for promiscuous recognition of several different hybrid insulin peptides (HIPs) by the highly diabetogenic, I-A g7 -restricted 4.1-T cell receptor (TCR). To understand the structural determinants of this phenomenon, we solved the structure of an agonistic HIP/I-A g7 complex, both in isolation as well as bound to the 4.1-TCR. We find that HIP promiscuity of the 4.1-TCR is dictated, on the one hand, by an amino acid sequence pattern that ensures I-A g7 binding and, on the other hand, by the presence of three acidic residues at positions P5, P7 and P8 that favor an optimal engagement by the 4.1-TCR's complementary determining regions. Surprisingly, comparison of the TCR-bound and unbound HIP/I-A g7 structures reveals that 4.1-TCR binding triggers several novel and unique structural motions in both the I-A g7 molecule and the peptide that are essential for docking. This observation indicates that the type 1 diabetes-associated I-A g7 molecule is structurally malleable and that this plasticity allows the recognition of multiple peptides by individual TCRs that would otherwise be unable to do so.


  • Organizational Affiliation

    Unit of Protein Crystallography and Structural Immunology, Navarrabiomed, Navarra, Spain.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
H-2 class II histocompatibility antigen, A-D alpha chain
A, C
202Mus musculusMutation(s): 1 
Gene Names: H2-Aa
UniProt
Find proteins for P04228 (Mus musculus)
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Go to UniProtKB:  P04228
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UniProt GroupP04228
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
H2-Ab1 protein
B, D
230Mus musculusMutation(s): 0 
Gene Names: H2-Ab1
UniProt
Find proteins for Q31135 (Mus musculus)
Explore Q31135 
Go to UniProtKB:  Q31135
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
4.1 TCR beta chain
E, F
242Mus musculusMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
4.1 TCR alpha chain
G, H
207Mus musculusMutation(s): 0 
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  • Reference Sequence

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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Hybrid insulin peptideI [auth T],
J [auth W]
15Mus musculusMutation(s): 0 
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
K [auth A],
M [auth B],
O [auth C],
P [auth C],
Q [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
EDO
Query on EDO

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L [auth A]
N [auth B]
R [auth D]
S [auth E]
U [auth G]
L [auth A],
N [auth B],
R [auth D],
S [auth E],
U [auth G],
W [auth G]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

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V [auth G]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

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T [auth F],
X [auth H]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 213.615α = 90
b = 133.457β = 103.69
c = 102.56γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Economy and CompetitivenessSpainRTI2018-093964-B-I00
Spanish Ministry of Science, Innovation, and UniversitiesSpainRYC-2017-21683
Spanish Ministry of Science, Innovation, and UniversitiesSpainPGC2018-094894-B-I00

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-20
    Type: Initial release
  • Version 1.1: 2022-08-10
    Changes: Database references
  • Version 1.2: 2022-08-17
    Changes: Database references
  • Version 1.3: 2022-08-24
    Changes: Database references
  • Version 1.4: 2024-01-31
    Changes: Data collection, Refinement description