8YDW

Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron XBB.1.5 variant spike protein in complex with CeSPIACE

• PDB DOI: https://doi.org/10.2210/pdb8YDW/pdb

• Classification: VIRAL PROTEIN/INHIBITOR
• Organism(s): synthetic construct, Severe acute respiratory syndrome coronavirus 2
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2024-02-21 Released: 2025-01-15 
• Deposition Author(s): Nakamura, S., Numoto, N., Fujiyoshi, Y.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED), Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.254 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.226 (DCC) 

Starting Model: experimental

Literature

Development of a short-peptide inhibiting any SARS-CoV-2 variants based on structural biology

Nakamura, S., Tanimura, Y., Nomura, R., Suzuki, H., Nishikawa, K., Kamegawa, A., Numoto, N., Tanaka, A., Kawabata, S., Sakaguchi, S., Emi, A., Suzuki, Y., Fujiyoshi, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 31.04 kDa 
• Atom Count: 1,969 
• Modelled Residue Count: 236 
• Deposited Residue Count: 269 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SARS-CoV-2 inhibiting peptide CeSPIACE	A	39	synthetic construct	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	B	230	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 22  Gene Names: S, 2
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
GOL	C [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	D [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.254 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.226 (DCC) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.76	α = 90
b = 74.76	β = 90
c = 100.07	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-15 
Deposition Author(s): Nakamura, S., Numoto, N., Fujiyoshi, Y.

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Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	JP21fk0108462, JP21fk0108585, JP21ae0121028, JP18ae0101046
Japan Society for the Promotion of Science (JSPS)	Japan	20H00451

Revision History  

• Version 1.0: 2025-01-15
  Type: Initial release