6Z9V | pdb_00006z9v

Human Class I Major Histocompatibility Complex, A02 allele, presenting IIGWMWIPV

PDB DOI: https://doi.org/10.2210/pdb6Z9V/pdb

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

Deposited: 2020-06-04 Released: 2021-06-30
Deposition Author(s): Rizkallah, P.J., Man, S., Redman, J.E.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free:
0.216 (Depositor), 0.222 (DCC)
R-Value Work:
0.176 (Depositor), 0.185 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Synthetic Peptides with Inadvertent Chemical Modifications Can Activate Potentially Autoreactive T Cells.

Man, S., Redman, J.E., Cross, D.L., Cole, D.K., Can, I., Davies, B., Hashimdeen, S.S., Reid, R., Llewellyn-Lacey, S., Miners, K.L., Ladell, K., Lissina, A., Brown, P.E., Wooldridge, L., Price, D.A., Rizkallah, P.J.

(2021) J Immunol 207: 1009-1017

PubMed: 34321228 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.4049/jimmunol.2000756
Primary Citation Related Structures:
6Z9V, 6Z9W, 6Z9X

PubMed Abstract:
The human CD8 ⁺ T cell clone 6C5 has previously been shown to recognize the tert -butyl-modified Bax _161-170 peptide LLSY(3- t Bu)FGTPT presented by HLA-A*02:01. This nonnatural epitope was likely created as a by-product of fluorenylmethoxycarbonyl protecting group peptide synthesis and bound poorly to HLA-A*02:01. In this study, we used a systematic approach to identify and characterize natural ligands for the 6C5 TCR. Functional analyses revealed that 6C5 T cells only recognized the LLSYFGTPT peptide when t Bu was added to the tyrosine residue and did not recognize the LLSYFGTPT peptide modified with larger (di- t Bu) or smaller chemical groups (Me). Combinatorial peptide library screening further showed that 6C5 T cells recognized a series of self-derived peptides with dissimilar amino acid sequences to LLSY(3- t Bu)FGTPT. Structural studies of LLSY(3- t Bu)FGTPT and two other activating nonamers (IIGWMWIPV and LLGWVFAQV) in complex with HLA-A*02:01 demonstrated similar overall peptide conformations and highlighted the importance of the position (P) 4 residue for T cell recognition, particularly the capacity of the bulky amino acid tryptophan to substitute for the t Bu-modified tyrosine residue in conjunction with other changes at P5 and P6. Collectively, these results indicated that chemical modifications directly altered the immunogenicity of a synthetic peptide via molecular mimicry, leading to the inadvertent activation of a T cell clone with unexpected and potentially autoreactive specificities.

Organizational Affiliation

Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom; ManS@cf.ac.uk.

Macromolecule Content

Total Structure Weight: 92.21 kDa
Atom Count: 7,063
Modeled Residue Count: 770
Deposited Residue Count: 770
Unique protein chains: 3

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen	A, D	276	Homo sapiens	Mutation(s): 0 Gene Names: HLA-A
UniProt
Find proteins for A0A140T913 (Homo sapiens) Explore A0A140T913 Go to UniProtKB: A0A140T913
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A140T913
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B, E	100	Homo sapiens	Mutation(s): 0 Gene Names: B2M, CDABP0092, HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens) Explore P61769 Go to UniProtKB: P61769
PHAROS: P61769 GTEx: ENSG00000166710
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61769
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ILE-ILE-GLY-TRP-MET-TRP-ILE-PRO-VAL	C, F	9	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PE8 Query on PE8 Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] MOL2 format, chain Z [auth D] mmCIF format, chain Z [auth D]	Z [auth D]	3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL C₁₆ H₃₄ O₉ GLZWNFNQMJAZGY-UHFFFAOYSA-N		Interactions Focus chain Z [auth D] Interactions & Density Focus chain Z [auth D]
P4G Query on P4G Download:Ideal Coordinates CCD File SDF format, chain Q [auth C] SDF format, chain Y [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain Y [auth D]	Q [auth C], Y [auth D]	1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE C₈ H₁₈ O₃ RRQYJINTUHWNHW-UHFFFAOYSA-N		Interactions Focus chain Q [auth C] Focus chain Y [auth D] Interactions & Density Focus chain Q [auth C] Focus chain Y [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain X [auth D] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain X [auth D] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain X [auth D]	J [auth A], K [auth A], L [auth A], X [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain X [auth D] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain X [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain EA [auth E] SDF format, chain I [auth A] SDF format, chain T [auth D] SDF format, chain U [auth D] SDF format, chain V [auth D] SDF format, chain W [auth D] MOL2 format, chain EA [auth E] MOL2 format, chain I [auth A] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] mmCIF format, chain EA [auth E] mmCIF format, chain I [auth A] mmCIF format, chain T [auth D] mmCIF format, chain U [auth D] mmCIF format, chain V [auth D] mmCIF format, chain W [auth D]	EA [auth E] I [auth A] T [auth D] U [auth D] V [auth D] EA [auth E], I [auth A], T [auth D], U [auth D], V [auth D], W [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain EA [auth E] Focus chain I [auth A] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Interactions & Density Focus chain EA [auth E] Focus chain I [auth A] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain CA [auth E] SDF format, chain DA [auth E] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth C] SDF format, chain R [auth D] SDF format, chain S [auth D] MOL2 format, chain BA [auth E] MOL2 format, chain CA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth C] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] mmCIF format, chain BA [auth E] mmCIF format, chain CA [auth E] mmCIF format, chain DA [auth E] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth C] mmCIF format, chain R [auth D] mmCIF format, chain S [auth D]	BA [auth E] CA [auth E] DA [auth E] G [auth A] H [auth A] BA [auth E], CA [auth E], DA [auth E], G [auth A], H [auth A], N [auth B], O [auth B], P [auth C], R [auth D], S [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain S [auth D] Interactions & Density Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain S [auth D]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain AA [auth E] MOL2 format, chain AA [auth E] mmCIF format, chain AA [auth E]	AA [auth E]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Interactions & Density Focus chain AA [auth E]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B] mmCIF format, chain M [auth B]	M [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]