7Z50 | pdb_00007z50

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

PDB DOI: https://doi.org/10.2210/pdb7Z50/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus
Expression System: Cricetulus griseus, Escherichia coli
Mutation(s): Yes

Deposited: 2022-03-06 Released: 2022-07-20
Deposition Author(s): Lopez-Sagaseta, J., Erausquin, E.
Funding Organization(s): Spanish Ministry of Economy and Competitiveness, Spanish Ministry of Science, Innovation, and Universities

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free:
0.261 (Depositor), 0.252 (DCC)
R-Value Work:
0.221 (Depositor)
R-Value Observed:
0.223 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

PubMed: 35967292 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.3389/fimmu.2022.924311
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 204.27 kDa
Atom Count: 12,716
Modeled Residue Count: 1,595
Deposited Residue Count: 1,792
Unique protein chains: 5

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H-2 class II histocompatibility antigen, A-D alpha chain	A, C	202	Mus musculus	Mutation(s): 1 Gene Names: H2-Aa
UniProt
Find proteins for P04228 (Mus musculus) Explore P04228 Go to UniProtKB: P04228
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04228
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain C
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
H2-Ab1 protein	B, D	230	Mus musculus	Mutation(s): 0 Gene Names: H2-Ab1
UniProt
Find proteins for Q31135 (Mus musculus) Explore Q31135 Go to UniProtKB: Q31135
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q31135
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B Focus chain D
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
4.1 TCR beta chain	E, F	242	Mus musculus	Mutation(s): 0

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
4.1 TCR alpha chain	G, H	207	Mus musculus	Mutation(s): 0

Find similar proteins by: Sequence | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Hybrid insulin peptide	I [auth T], J [auth W]	15	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain M [auth B] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth D] MOL2 format, chain K [auth A] MOL2 format, chain M [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth D] mmCIF format, chain K [auth A] mmCIF format, chain M [auth B] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth D]	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		Interactions Focus chain K [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth D] Interactions & Density Focus chain K [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain N [auth B] SDF format, chain R [auth D] SDF format, chain S [auth E] SDF format, chain U [auth G] SDF format, chain W [auth G] MOL2 format, chain L [auth A] MOL2 format, chain N [auth B] MOL2 format, chain R [auth D] MOL2 format, chain S [auth E] MOL2 format, chain U [auth G] MOL2 format, chain W [auth G] mmCIF format, chain L [auth A] mmCIF format, chain N [auth B] mmCIF format, chain R [auth D] mmCIF format, chain S [auth E] mmCIF format, chain U [auth G] mmCIF format, chain W [auth G]	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		Interactions Focus chain L [auth A] Focus chain N [auth B] Focus chain R [auth D] Focus chain S [auth E] Focus chain U [auth G] Focus chain W [auth G] Interactions & Density Focus chain L [auth A] Focus chain N [auth B] Focus chain R [auth D] Focus chain S [auth E] Focus chain U [auth G] Focus chain W [auth G]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain V [auth G] MOL2 format, chain V [auth G] mmCIF format, chain V [auth G]	V [auth G]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain V [auth G] Interactions & Density Focus chain V [auth G]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain T [auth F] SDF format, chain X [auth H] MOL2 format, chain T [auth F] MOL2 format, chain X [auth H] mmCIF format, chain T [auth F] mmCIF format, chain X [auth H]	T [auth F], X [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain T [auth F] Focus chain X [auth H] Interactions & Density Focus chain T [auth F] Focus chain X [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.261 (Depositor), 0.252 (DCC)
R-Value Work: 0.221 (Depositor)
R-Value Observed: 0.223 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 213.615	α = 90
b = 133.457	β = 103.69
c = 102.56	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-07-20

Deposition Author(s):

Lopez-Sagaseta, J.

Erausquin, E.

Funding Organization	Location	Grant Number
Spanish Ministry of Economy and Competitiveness	Spain	RTI2018-093964-B-I00
Spanish Ministry of Science, Innovation, and Universities	Spain	RYC-2017-21683
Spanish Ministry of Science, Innovation, and Universities	Spain	PGC2018-094894-B-I00