7PBE | pdb_00007pbe

Emergence of immune escape at dominant SARS-CoV-2 killer T-cell epitope

• PDB DOI: https://doi.org/10.2210/pdb7PBE/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-08-02 Released: 2022-04-27 
• Deposition Author(s): Rizkallah, P.J., Sewell, A.K., Wall, A., Fuller, A.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.296 (Depositor), 0.291 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.229 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Starting Model: experimental

Literature

Emergence of immune escape at dominant SARS-CoV-2 killer T cell epitope.

Dolton, G., Rius, C., Hasan, M.S., Wall, A., Szomolay, B., Behiry, E., Whalley, T., Southgate, J., Fuller, A., Morin, T., Topley, K., Tan, L.R., Goulder, P.J.R., Spiller, O.B., Rizkallah, P.J., Jones, L.C., Connor, T.R., Sewell, A.K.

(2022) Cell 185: 2936

• PubMed: 35931021 
• DOI: https://doi.org/10.1016/j.cell.2022.07.002
• Primary Citation Related Structures: 
  7P3D, 7P3E, 7PBE


• PubMed Abstract: 
  

  We studied the prevalent cytotoxic CD8 T cell response mounted against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike glycoprotein _269-277 epitope (sequence YLQPRTFLL) via the most frequent human leukocyte antigen (HLA) class I worldwide, HLA A ^∗ 02. The Spike P272L mutation that has arisen in at least 112 different SARS-CoV-2 lineages to date, including in lineages classified as "variants of concern," was not recognized by the large CD8 T cell response seen across cohorts of HLA A ^∗ 02 ⁺ convalescent patients and individuals vaccinated against SARS-CoV-2, despite these responses comprising of over 175 different individual T cell receptors. Viral escape at prevalent T cell epitopes restricted by high frequency HLAs may be particularly problematic when vaccine immunity is focused on a single protein such as SARS-CoV-2 Spike, providing a strong argument for inclusion of multiple viral proteins in next generation vaccines and highlighting the need for monitoring T cell escape in new SARS-CoV-2 variants.

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Organizational Affiliation: 
• Division of Infection and Immunity, Cardiff University School of Medicine, CF14 4XN Cardiff, Wales, UK.
Division of Infection and Immunity, Cardiff University School of Medicine, CF14 4XN Cardiff, Wales, UK; Systems Immunology Research Institute, Cardiff University, CF14 4XN Cardiff, Wales, UK.
School of Biosciences, Cardiff University, CF10 3AX Cardiff, Wales, UK.
Department of Paediatrics, University of Oxford, OX3 9DU Oxford, England, UK.
Division of Infection and Immunity, Cardiff University School of Medicine, CF14 4XN Cardiff, Wales, UK; Centre for Clinical Research, Royal Glamorgan Hospital, Ynysmaerdy CF72 8XR, UK.
Systems Immunology Research Institute, Cardiff University, CF14 4XN Cardiff, Wales, UK; School of Biosciences, Cardiff University, CF10 3AX Cardiff, Wales, UK; Pathogen genomics Unit, Public Health Wales NHS Trust, CF14 4XW Cardiff, Wales, UK. Electronic address: [e-mail].
Division of Infection and Immunity, Cardiff University School of Medicine, CF14 4XN Cardiff, Wales, UK; Systems Immunology Research Institute, Cardiff University, CF14 4XN Cardiff, Wales, UK. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: homology

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 191.54 kDa 
• Atom Count: 13,403 
• Modeled Residue Count: 1,652 
• Deposited Residue Count: 1,662 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen	A, F	276	Homo sapiens	Mutation(s): 0  Gene Names: HLA-A
UniProt
Find proteins for A0A140T913 (Homo sapiens) Explore A0A140T913  Go to UniProtKB:  A0A140T913

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B, G	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 ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	C, H	9	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Human T-cell Receptor YLQ36, alpha chain	D, I	203	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Human T-cell Receptor YLQ36, beta chain	E, J	243	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	K [auth A], O [auth F]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	L [auth A], M [auth B], N [auth E], P [auth F], Q [auth I]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.296 (Depositor), 0.291 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.229 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 229.24	α = 90
b = 46.45	β = 96.75
c = 184.72	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction
DIALS	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-04-27 
Deposition Author(s): Rizkallah, P.J., Sewell, A.K., Wall, A., Fuller, A.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-04-27
  Type: Initial release
  
• Version 1.1: 2022-07-27
  Changes: Database references
• Version 1.2: 2022-08-17
  Changes: Database references
• Version 1.3: 2024-01-31
  Changes: Data collection, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary