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 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.221 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.223 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 1.5 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
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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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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UniProt GroupQ31135
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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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

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

Download Ideal Coordinates CCD File 
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 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.221 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.223 (Depositor) 
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

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view details

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
  • Version 1.5: 2024-10-16
    Changes: Structure summary