7UM2 | pdb_00007um2

SARS-CoV-2 Spike-derived peptide S417-425 K417T mutant (TIADYNYKL) presented by HLA-A*02:01

• PDB DOI: https://doi.org/10.2210/pdb7UM2/pdb

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


• Deposited: 2022-04-06 Released: 2023-04-26 
• Deposition Author(s): Szeto, C., Gras, S.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 
  0.195 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

SARS-CoV-2 Spike-derived peptide S417-425 K417T mutant (TIADYNYKL) presented by HLA-A*02:01

Szeto, C., Gras, S.

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: 54.16 kDa 
• Atom Count: 3,523 
• Modeled Residue Count: 385 
• Deposited Residue Count: 474 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class I antigen	A	365	Homo sapiens	Mutation(s): 0  Gene Names: HLA-A, HLA
UniProt
Find proteins for Q53Z42 (Homo sapiens) Explore Q53Z42  Go to UniProtKB:  Q53Z42

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
SARS-CoV-2 Spike-derived peptide S417-425 K417T mutant (TIADYNYKL)	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD	E [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
ZN	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA	F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free:  0.195 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.171	α = 90
b = 79.105	β = 90
c = 110.86	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-04-26 
Deposition Author(s): Szeto, C., Gras, S.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-04-26
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary