4GKZ | pdb_00004gkz

HA1.7, a MHC class II restricted TCR specific for haemagglutinin

PDB DOI: https://doi.org/10.2210/pdb4GKZ/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-08-13 Released: 2012-11-07
Deposition Author(s): Holland, C.J., Rizkallah, P.J., Cole, D.K., Sewell, A.K., Godkin, A.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free:
0.298 (Depositor), 0.294 (DCC)
R-Value Work:
0.249 (Depositor), 0.237 (DCC)
R-Value Observed:
0.251 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Minimal conformational plasticity enables TCR cross-reactivity to different MHC class II heterodimers.

Holland, C.J., Rizkallah, P.J., Vollers, S., Calvo-Calle, J.M., Madura, F., Fuller, A., Sewell, A.K., Stern, L.J., Godkin, A., Cole, D.K.

(2012) Sci Rep 2: 629-629

PubMed: 22953050 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/srep00629
Primary Citation Related Structures:
4GKZ

PubMed Abstract:
Successful immunity requires that a limited pool of αβ T-cell receptors (TCRs) provide cover for a vast number of potential foreign peptide antigens presented by 'self' major histocompatibility complex (pMHC) molecules. Structures of unligated and ligated MHC class-I-restricted TCRs with different ligands, supplemented with biophysical analyses, have revealed a number of important mechanisms that govern TCR mediated antigen recognition. HA1.7 TCR binding to the influenza hemagglutinin antigen (HA(306-318)) presented by HLA-DR1 or HLA-DR4 represents an ideal system for interrogating pMHC-II antigen recognition. Accordingly, we solved the structure of the unligated HA1.7 TCR and compared it to both complex structures. Despite a relatively rigid binding mode, HA1.7 T-cells could tolerate mutations in key contact residues within the peptide epitope. Thermodynamic analysis revealed that limited plasticity and extreme favorable entropy underpinned the ability of the HA1.7 T-cell clone to cross-react with HA(306-318) presented by multiple MHC-II alleles.

Organizational Affiliation

Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom.

Macromolecule Content

Total Structure Weight: 50.63 kDa
Atom Count: 3,626
Modeled Residue Count: 443
Deposited Residue Count: 443
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha chain of Class II TCR	A	202	Homo sapiens	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta Chain of Class II TCR	B	241	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TAM Query on TAM Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	TRIS(HYDROXYETHYL)AMINOMETHANE C₇ H₁₇ N O₃ GKODZWOPPOTFGA-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	G [auth A], H [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] J [auth B] C [auth A], D [auth A], E [auth A], F [auth A], J [auth B], K [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free: 0.298 (Depositor), 0.294 (DCC)
R-Value Work: 0.249 (Depositor), 0.237 (DCC)
R-Value Observed: 0.251 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.24	α = 90
b = 49.66	β = 94.33
c = 72.61	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
GDA	data collection
xia2	data reduction

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-11-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-11-07
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-11-27
Changes: Structure summary