6Z9V

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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

  • DOI: https://doi.org/10.4049/jimmunol.2000756
  • Primary Citation of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MHC class I antigen
A, D
276Homo sapiensMutation(s): 0 
Gene Names: HLA-A
UniProt
Find proteins for A0A140T913 (Homo sapiens)
Explore A0A140T913 
Go to UniProtKB:  A0A140T913
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A140T913
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin
B, E
100Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61769
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ILE-ILE-GLY-TRP-MET-TRP-ILE-PRO-VAL
C, F
9Homo sapiensMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PE8
Query on PE8

Download Ideal Coordinates CCD File 
Z [auth D]3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL
C16 H34 O9
GLZWNFNQMJAZGY-UHFFFAOYSA-N
P4G
Query on P4G

Download Ideal Coordinates CCD File 
Q [auth C],
Y [auth D]
1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE
C8 H18 O3
RRQYJINTUHWNHW-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
J [auth A],
K [auth A],
L [auth A],
X [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
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
EDO
Query on EDO

Download Ideal Coordinates CCD File 
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
CA
Query on CA

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AA [auth E]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA
Query on NA

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M [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 
  • Space Group: P 32 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.19α = 90
b = 85.19β = 90
c = 232.55γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom509517

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-30
    Type: Initial release
  • Version 1.1: 2021-08-11
    Changes: Database references
  • Version 1.2: 2021-09-29
    Changes: Data collection, Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-11-13
    Changes: Structure summary