Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1BC 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: homology

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1BC 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 92.17 kDa 
• Atom Count: 6784 
• Residue Count: 777 
• Unique protein chains: 4

6HBY

HLA class II peptide flanking residues tune the immunogenicity of a human tumor-derived epitope

• DOI: 10.2210/pdb6HBY/pdb

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


• Deposited: 2018-08-13 Released: 2019-08-14 
• Deposition Author(s): MacLachlan, B., Rizkallah, P.J., Sewell, A.K., Cole, D.K., Godkin, A.J.
• Funding Organization(s): Cancer Research UK

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.241 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 

Literature

Human leukocyte antigen (HLA) class II peptide flanking residues tune the immunogenicity of a human tumor-derived epitope.

MacLachlan, B.J., Dolton, G., Papakyriakou, A., Greenshields-Watson, A., Mason, G.H., Schauenburg, A., Besneux, M., Szomolay, B., Elliott, T., Sewell, A.K., Gallimore, A., Rizkallah, P., Cole, D.K., Godkin, A.

(2019) J Biol Chem 294: 20246-20258

• PubMed: 31619516 
• DOI: 10.1074/jbc.RA119.009437
• Structures With Same Primary Citation


• PubMed Abstract: 
  

CD4 ⁺ T-cells recognize peptide antigens, in the context of human leukocyte antigen (HLA) class II molecules (HLA-II), which through peptide-flanking residues (PFRs) can extend beyond the limits of the HLA binding. The role of the PFRs during antigen recognition is not fully understood; however, recent studies have indicated that these regions can influence T-cell receptor (TCR) affinity and pHLA-II stability. Here, using various biochemical approaches including peptide sensitivity ELISA and ELISpot assays, peptide-binding assays and HLA-II tetramer staining, we focused on CD4 ⁺ T-cell responses against a tumor antigen, 5T4 oncofetal trophoblast glycoprotein (5T4), which have been associated with improved control of colorectal cancer. Despite their weak TCR-binding affinity, we found that anti-5T4 CD4 ⁺ T-cells are polyfunctional and that their PFRs are essential for TCR recognition of the core bound nonamer. The high-resolution (1.95 Å) crystal structure of HLA-DR1 presenting the immunodominant 20-mer peptide 5T4 _111-130 , combined with molecular dynamic simulations, revealed how PFRs explore the HLA-proximal space to contribute to antigen reactivity. These findings advance our understanding of what constitutes an HLA-II epitope and indicate that PFRs can tune weak affinity TCR-pHLA-II interactions.

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Organizational Affiliation: 

Department of Gastroenterology and Hepatology, University Hospital of Wales, CF14 4XN Cardiff, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
HLA class II histocompatibility antigen, DR alpha chain	A	178	Homo sapiens	Mutation(s): 0  Gene Names: HLA-DRA, HLA-DRA1
Find proteins for P01903 (Homo sapiens) Go to UniProtKB:  P01903
NIH Common Fund Data Resources
PHAROS  P01903 GTEx  ENSG00000204287

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
HLA class II histocompatibility antigen, DRB1-1 beta chain	B, E	191	Homo sapiens	Mutation(s): 0  Gene Names: HLA-DRB1
Find proteins for P01911 (Homo sapiens) Go to UniProtKB:  P01911
NIH Common Fund Data Resources
PHAROS  P01911 GTEx  ENSG00000196126

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
ARRPPLAELAALNLSGSRL 5T4 tumour epitope	C, F	19	Homo sapiens	Mutation(s): 0  Gene Names: TPBG, 5T4
Find proteins for Q13641 (Homo sapiens) Go to UniProtKB:  Q13641
NIH Common Fund Data Resources
PHAROS  Q13641 GTEx  ENSG00000146242

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
HLA class II histocompatibility antigen, DR alpha chain	D	180	Homo sapiens	Mutation(s): 0  Gene Names: HLA-DRA, HLA-DRA1
Find proteins for P01903 (Homo sapiens) Go to UniProtKB:  P01903
NIH Common Fund Data Resources
PHAROS  P01903 GTEx  ENSG00000204287

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	A, B, E	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO	A, B, D, E	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.241 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.96	α = 90
b = 121.29	β = 107.3
c = 68.96	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-08-13 
• Released Date: 2019-08-14 
Deposition Author(s): MacLachlan, B., Rizkallah, P.J., Sewell, A.K., Cole, D.K., Godkin, A.J.

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Funding Organization	Location	Grant Number
Cancer Research UK	United Kingdom	--

Revision History 

• Version 1.0: 2019-08-14
  Type: Initial release
  
• Version 1.1: 2019-10-30
  Changes: Data collection, Database references
• Version 1.2: 2020-01-08
  Changes: Database references
• Version 1.3: 2020-01-29
  Changes: Derived calculations