8HN4 | pdb_00008hn4

Complex structure of HLA2402 with recognizing SARS-CoV-2 epitope QYIKWPWYI

• PDB DOI: https://doi.org/10.2210/pdb8HN4/pdb

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


• Deposited: 2022-12-07 Released: 2023-12-27 
• Deposition Author(s): Deng, S.S., Jin, T.C., Xu, Z.H.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 
  0.251 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.205 (DCC) 

Starting Model: experimental

Literature

Immune escape at SARS- CoV-2 killer T cell epitope

Deng, S.S., Jin, T.C., Xu, Z.H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 48.61 kDa 
• Atom Count: 3,156 
• Modeled Residue Count: 383 
• Deposited Residue Count: 417 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen	A	308	Homo sapiens	Mutation(s): 0  Gene Names: HLA-A
UniProt
Find proteins for F6IR24 (Homo sapiens) Explore F6IR24  Go to UniProtKB:  F6IR24

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	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
SARS-CoV-2 T-cell epitope QYIKWPWYI	C [auth E]	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free:  0.251 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.205 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.066	α = 90
b = 67.246	β = 90
c = 116.79	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-12-27 
Deposition Author(s): Deng, S.S., Jin, T.C., Xu, Z.H.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	82272301

Revision History  

• Version 1.0: 2023-12-27
  Type: Initial release
  
• Version 1.1: 2024-10-30
  Changes: Structure summary