Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 211.57 kDa 
• Atom Count: 6,607 
• Modelled Residue Count: 791 
• Deposited Residue Count: 1,853 
• Unique protein chains: 2

 8IOV

Structure of SARS-CoV-2 XBB.1 spike RBD in complex with ACE2

• PDB DOI:  https://doi.org/10.2210/pdb8IOV/pdb
• EM Map EMD-35626: EMDB EMDataResource

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


• Deposited: 2023-03-13 Released: 2023-05-24 
• Deposition Author(s): Anraku, Y., Kita, S., Yajima, H., 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: 3.29 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Virological characteristics of the SARS-CoV-2 XBB variant derived from recombination of two Omicron subvariants

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., Ito, H., Misawa, N., Kimura, I., Suganami, M., Chiba, M., Yoshimura, R., Yasuda, K., Iida, K., Ohsumi, N., Strange, A.P., Takahashi, O., Ichihara, K., Shibatani, Y., Nishiuchi, T., Kato, M., Ferdous, Z., Mouri, H., Shishido, K., Sawa, H., Hashimoto, R., Watanabe, Y., Sakamoto, A., Yasuhara, N., Suzuki, T., Kimura, K., Nakajima, Y., Nakagawa, S., Wu, J., Shirakawa, K., Takaori-Kondo, A., Nagata, K., Kazuma, Y., Nomura, R., Horisawa, Y., Tashiro, Y., Kawai, Y., Irie, T., Kawabata, R., Motozono, C., Toyoda, M., Ueno, T., Hashiguchi, T., Ikeda, T., Fukuhara, T., Saito, A., Tanaka, S., Matsuno, K., Takayama, K., Sato, K.

(2023) Nat Commun 14: 2800

• DOI: https://doi.org/10.1038/s41467-023-38435-3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Processed angiotensin-converting enzyme 2	A	608	Homo sapiens	Mutation(s): 0  Gene Names: ACE2, UNQ868/PRO1885 EC: 3.4.17.23 (UniProt), 3.4.17 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYF1 (Homo sapiens) Explore Q9BYF1  Go to UniProtKB:  Q9BYF1
PHAROS:  Q9BYF1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	B	1,245	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 47  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: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D	2		N-Glycosylation

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	3		N-Glycosylation

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F	5		N-Glycosylation

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	G [auth A], H [auth A], I [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.29 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.1.2
MODEL REFINEMENT	PHENIX	1.20

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-05-24 
Deposition Author(s): Anraku, Y., Kita, S., Yajima, H., 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: 2023-05-24
  Type: Initial release