8IF1

Complex structure of HLA2402 with recognizing SARS-CoV-2 Y453F epitope NYNYLFRLF

• PDB DOI: https://doi.org/10.2210/pdb8IF1/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-02-16 Released: 2024-02-21 
• Deposition Author(s): Deng, S.S., Jin, T.C., Xu, Z.H., Wang, M.H.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.309 
• R-Value Work: 0.251 

Literature

Complex structure of HLA-A*24:02 and SARS-Cov-2 epitope NYNYLFRLF with Y453F mutation

Deng, S.S., Jin, T.C., Xu, Z.H., Wang, M.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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 146.05 kDa 
• Atom Count: 9,528 
• Modelled Residue Count: 1,160 
• Deposited Residue Count: 1,254 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen	A, D [auth C], G	308	Homo sapiens	Mutation(s): 0  Gene Names: HLA-A
UniProt
Find proteins for D9UAY1 (Homo sapiens) Explore D9UAY1  Go to UniProtKB:  D9UAY1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B, E [auth D], H	101	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 [auth E], F, I	9	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1
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: 2.50 Å
• R-Value Free: 0.309 
• R-Value Work: 0.251 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.05	α = 90
b = 167.49	β = 90
c = 168.58	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-02-21 
Deposition Author(s): Deng, S.S., Jin, T.C., Xu, Z.H., Wang, M.H.

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

Revision History  

• Version 1.0: 2024-02-21
  Type: Initial release