7LG0 | pdb_00007lg0

Human leukocyte antigen B*07:02 in complex with SARS-CoV2 epitope SPRWYFYYL

• PDB DOI: https://doi.org/10.2210/pdb7LG0/pdb

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


• Deposited: 2021-01-19 Released: 2021-02-03 
• Deposition Author(s): Patskovska, L., Patskovsky, Y., Krogsgaard, M.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.268 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Human leukocyte antigen B*07:02 in complex with SARS-CoV2 epitope SPRWYFYYL

Patskovska, L., Patskovsky, Y., Krogsgaard, M.

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: 45.42 kDa 
• Atom Count: 3,384 
• Modeled Residue Count: 384 
• Deposited Residue Count: 384 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class I histocompatibility antigen, B-7 alpha chain	A	275	Homo sapiens	Mutation(s): 0  Gene Names: HLA-B, HLAB
UniProt & NIH Common Fund Data Resources
Find proteins for P01889 (Homo sapiens) Explore P01889  Go to UniProtKB:  P01889
PHAROS:  P01889 GTEx:  ENSG00000234745

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
Nucleoprotein	C	9	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0
UniProt
Find proteins for P59595 (Severe acute respiratory syndrome coronavirus) Explore P59595  Go to UniProtKB:  P59595

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P6G	D [auth A]	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.268 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.723	α = 90
b = 155.172	β = 90
c = 88.165	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-02-03 
Deposition Author(s): Patskovska, L., Patskovsky, Y., Krogsgaard, M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	CA243486-01A1

Revision History  

• Version 1.0: 2021-02-03
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Advisory, Data collection, Database references, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary