8JYM

Structure of the SARS-CoV-2 XBB.1.5 spike glycoprotein (closed state 2)

• PDB DOI: https://doi.org/10.2210/pdb8JYM/pdb
• EM Map EMD-36726: EMDB EMDataResource

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


• Deposited: 2023-07-03 Released: 2024-01-03 
• Deposition Author(s): Yajima, H., Anraku, Y., Kita, S., Kimura, K., Sasaki, J., Sasaki-Tabata, K., Maenaka, K., Hashiguchi, T.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED), Japan Science and Technology, Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.79 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Virological characteristics of the SARS-CoV-2 XBB.1.5 variant

Tamura, T., Ito, J., Uriu, K., Zahradnik, J., Kida, I., Anraku, Y., Nasser, H., Shofa, M., Oda, Y., Lytras, S., Nao, N., Itakura, Y., Deguchi, S., Suzuki, R., Wang, L., Begum, M.M., Kita, S., Yajima, H., Sasaki, J., Sasaki-Tabata, K., Shimizu, R., Tsuda, M., Kosugi, Y., Fujita, S., Pan, L., Sauter, D., Yoshimatsu, K., Suzuki, S., Asakura, H., Nagashima, M., Sadamasu, K., Yoshimura, K., Yamamoto, Y., Nagamoto, T., Schreiber, G., Maenaka, K., Hashiguchi, T., Ikeda, T., Fukuhara, T., Saito, A., Tanaka, S., Matsuno, K., Takayama, K., Sato, K.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 141.59 kDa 
• Atom Count: 8,308 
• Modelled Residue Count: 1,033 
• Deposited Residue Count: 1,245 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A	1,245	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 45  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B, C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.79 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	Coot	0.9.8.7
MODEL REFINEMENT	PHENIX	1.20.1
RECONSTRUCTION	cryoSPARC	4.1.2

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-01-03 
Deposition Author(s): Yajima, H., Anraku, Y., Kita, S., Kimura, K., Sasaki, J., Sasaki-Tabata, K., Maenaka, K., Hashiguchi, T.

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Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	JP21am0101093
Japan Agency for Medical Research and Development (AMED)	Japan	JP22ama121037
Japan Science and Technology	Japan	JPMJCR20H8
Japan Society for the Promotion of Science (JSPS)	Japan	JPJSCCA20190008
Japan Society for the Promotion of Science (JSPS)	Japan	20H05773
Japan Society for the Promotion of Science (JSPS)	Japan	JP20H05873

Revision History  

• Version 1.0: 2024-01-03
  Type: Initial release