8Z05

The structure of HLA-A/peptide from virus

• PDB DOI: https://doi.org/10.2210/pdb8Z05/pdb

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


• Deposited: 2024-04-09 Released: 2025-01-29 
• Deposition Author(s): Zhang, J.N., Tian, J.M., Liu, J.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 
  0.275 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: experimental

Literature

Further cytotoxic T cell escapes of SARS-CoV-2 JN.1 explain its dominant circulation in recent waves

Tian, J.M., Shang, B.L., Zhang, J.N., Liu, J.

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)

Macromolecule Content

• Total Structure Weight: 44.57 kDa 
• Atom Count: 3,269 
• Modelled Residue Count: 382 
• Deposited Residue Count: 382 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class I histocompatibility antigen, A alpha chain	A	274	Homo sapiens	Mutation(s): 0  Gene Names: HLA-A
UniProt
Find proteins for A0A140T955 (Homo sapiens) Explore A0A140T955  Go to UniProtKB:  A0A140T955

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	99	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 S2'	C	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: 1.96 Å
• R-Value Free:  0.275 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.885	α = 90
b = 53.318	β = 94.41
c = 84.449	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-29 
Deposition Author(s): Zhang, J.N., Tian, J.M., Liu, J.

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

Revision History  

• Version 1.0: 2025-01-29
  Type: Initial release