8UTC | pdb_00008utc

HUMAN LEUKOCYTE ANTIGEN B*07:02 IN COMPLEX WITH SARS-COV2 EPITOPE N105-113 (Y111F mutant)

• PDB DOI: https://doi.org/10.2210/pdb8UTC/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2023-10-30 Released: 2025-03-19 
• Deposition Author(s): Oltean, N., Nyovanie, S., Hashem, A., Patskovska, L., Patskovsky, Y., Krogsgaard, M.
• Funding Organization(s): National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

HUMAN LEUKOCYTE ANTIGEN B*07:02 IN COMPLEX WITH SARS-COV2 EPITOPE N105-113 (Y111F mutant)

Oltean, N., Nyovanie, S., Hashem, A., 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 2  

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

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

Macromolecule Content 

• Total Structure Weight: 91.15 kDa 
• Atom Count: 6,652 
• Modeled Residue Count: 768 
• Deposited Residue Count: 770 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class I histocompatibility antigen, B alpha chain	A, C	276	Homo sapiens	Mutation(s): 0  Gene Names: HLA-B
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, D	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	E, F	9	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1
UniProt
Find proteins for P0DTC9 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC9  Go to UniProtKB:  P0DTC9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	H [auth A], L [auth C]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE	G [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
CL	I [auth A], J [auth B], K [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.067	α = 90
b = 84.737	β = 90
c = 154.189	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data scaling
Aimless	data scaling
PHASER	phasing
REFMAC	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-19 
Deposition Author(s): Oltean, N., Nyovanie, S., Hashem, A., Patskovska, L., Patskovsky, Y., Krogsgaard, M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)	United States	UL1-TR001445-06-A1-S1

Revision History  

• Version 1.0: 2025-03-19
  Type: Initial release