7M8U

Crystal Structure of HLA-B*35:01 in complex with IPFAMQMAY, an 9-mer epitope from SARS-CoV-2 spike (S896-904)

• PDB DOI: https://doi.org/10.2210/pdb7M8U/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-03-30 Released: 2021-06-23 
• Deposition Author(s): Gras, S., Nguyen, A.T., Szeto, C.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.229 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 

Starting Model: experimental

Literature

SARS-CoV-2 Spike-Derived Peptides Presented by HLA Molecules

Nguyen, A.T., Szeto, C., Jayasinghe, D., Lobos, C.A., Halim, H., Chatzileontiadou, D.S.M., Grant, E.J., Gras, S.

(2021) Biophysica 1

• DOI: https://doi.org/10.3390/biophysica1020015

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: 45.24 kDa 
• Atom Count: 3,590 
• Modelled Residue Count: 384 
• Deposited Residue Count: 386 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class I histocompatibility antigen B, alpha chain	A	277	Homo sapiens	Mutation(s): 0  Gene Names: HLA-B
UniProt
Find proteins for Q546I9 (Homo sapiens) Explore Q546I9  Go to UniProtKB:  Q546I9

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
Spike protein S2 peptide	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	D [auth A], E [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
NA	F [auth A], G [auth A], H [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.229 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.238	α = 90
b = 82.38	β = 90
c = 111.011	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
BUSTER	refinement
PDB_EXTRACT	data extraction
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-06-23 
Deposition Author(s): Gras, S., Nguyen, A.T., Szeto, C.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	1159272

Revision History  

• Version 1.0: 2021-06-23
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary