8JYO | pdb_00008jyo

Structure of SARS-CoV-2 XBB.1.5 spike glycoprotein in complex with ACE2 (2-up state)

• PDB DOI: https://doi.org/10.2210/pdb8JYO/pdb
• EM Map EMD-36728: EMDB EMDataResource

• Classification: VIRAL PROTEIN/PROTEIN BINDING
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
• 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: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental

Literature

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

Tamura, T., Irie, T., Deguchi, S., Yajima, H., Tsuda, M., Nasser, H., Mizuma, K., Plianchaisuk, A., Suzuki, S., Uriu, K., Begum, M.M., Shimizu, R., Jonathan, M., Suzuki, R., Kondo, T., Ito, H., Kamiyama, A., Yoshimatsu, K., Shofa, M., Hashimoto, R., Anraku, Y., Kimura, K.T., Kita, S., Sasaki, J., Sasaki-Tabata, K., Maenaka, K., Nao, N., Wang, L., Oda, Y., Ikeda, T., Saito, A., Matsuno, K., Ito, J., Tanaka, S., Sato, K., Hashiguchi, T., Takayama, K., Fukuhara, T.

(2024) Nat Commun 15: 1176-1176

• PubMed: 38332154 
• DOI: https://doi.org/10.1038/s41467-024-45274-3
• Primary Citation of Related Structures:  
  8JYK, 8JYM, 8JYN, 8JYO, 8JYP


• PubMed Abstract: 
  

  Circulation of SARS-CoV-2 Omicron XBB has resulted in the emergence of XBB.1.5, a new Variant of Interest. Our phylogenetic analysis suggests that XBB.1.5 evolved from XBB.1 by acquiring the S486P spike (S) mutation, subsequent to the acquisition of a nonsense mutation in ORF8. Neutralization assays showed similar abilities of immune escape between XBB.1.5 and XBB.1. We determine the structural basis for the interaction between human ACE2 and the S protein of XBB.1.5, showing similar overall structures between the S proteins of XBB.1 and XBB.1.5. We provide the intrinsic pathogenicity of XBB.1 and XBB.1.5 in hamsters. Importantly, we find that the ORF8 nonsense mutation of XBB.1.5 resulted in impairment of MHC suppression. In vivo experiments using recombinant viruses reveal that the XBB.1.5 mutations are involved with reduced virulence of XBB.1.5. Together, our study identifies the two viral functions defined the difference between XBB.1 and XBB.1.5.

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Organizational Affiliation: 
• Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan.
Graduate School of Medicine, Hokkaido University, Sapporo, Japan.
School of Medicine, Hokkaido University, Sapporo, Japan.
Institute for the Advancement of Higher Education, Hokkaido University, Sapporo, Japan.
Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan.
One Health Research Center, Hokkaido University, Sapporo, Japan.
Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan.
Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan.
Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan.
Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan.
Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan.
Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan.
Department of Clinical Pathology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt.
Division of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan.
Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan.
Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan.
Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Japan.
Laboratory of Biomolecular Science and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan.
Department of Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan.
Division of Pathogen Structure, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan.
Global Station for Biosurfaces and Drug Discovery, Hokkaido University, Sapporo, Japan.
Division of International Research Promotion, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan.
Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan.
International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan.
International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan. [e-mail].
Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan. [e-mail].
Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan. [e-mail].
Graduate School of Medicine, The University of Tokyo, Tokyo, Japan. [e-mail].
International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan. [e-mail].
Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan. [e-mail].
CREST, Japan Science and Technology Agency, Kawaguchi, Japan. [e-mail].
International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan. [e-mail].
Collaboration Unit for Infection, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan. [e-mail].
Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan. [e-mail].
Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan. [e-mail].
Kyoto University Immunomonitoring Center, Kyoto University, Kyoto, Japan. [e-mail].
Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan. [e-mail].
AMED-CREST, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan. [e-mail].
Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan. [e-mail].
Graduate School of Medicine, Hokkaido University, Sapporo, Japan. [e-mail].
School of Medicine, Hokkaido University, Sapporo, Japan. [e-mail].
Institute for the Advancement of Higher Education, Hokkaido University, Sapporo, Japan. [e-mail].
Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan. [e-mail].
One Health Research Center, Hokkaido University, Sapporo, Japan. [e-mail].
Kyoto University Immunomonitoring Center, Kyoto University, Kyoto, Japan. [e-mail].
Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Japan. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A3B2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 571.33 kDa 
• Atom Count: 34,233 
• Modeled Residue Count: 4,193 
• Deposited Residue Count: 4,951 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	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
Glycosylation
Glycosylation Sites: 14		Go to GlyGen: P0DTC2-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Processed angiotensin-converting enzyme 2	D [auth E], E [auth D]	608	Homo sapiens	Mutation(s): 0  Gene Names: ACE2, UNQ868/PRO1885 EC: 3.4.17 (UniProt), 3.4.17.23 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYF1 (Homo sapiens) Explore Q9BYF1  Go to UniProtKB:  Q9BYF1
PHAROS:  Q9BYF1 GTEx:  ENSG00000130234
Glycosylation
Glycosylation Sites: 6		Go to GlyGen: Q9BYF1-1

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F, G, H, I, J, K, L, M, P	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	N, Q	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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	O, R	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	AA [auth A], AB [auth C], BA [auth A], BB [auth C], CA [auth A], CB [auth E], DA [auth A], DB [auth E], EA [auth A], EB [auth E], FA [auth B], FB [auth D], GA [auth B], GB [auth D], HA [auth B], HB [auth D], IA [auth B], JA [auth B], KA [auth B], LA [auth B], MA [auth B], NA [auth B], OA [auth B], PA [auth B], QA [auth B], RA [auth C], S [auth A], SA [auth C], T [auth A], TA [auth C], U [auth A], UA [auth C], V [auth A], VA [auth C], W [auth A], WA [auth C], X [auth A], XA [auth C], Y [auth A], YA [auth C], Z [auth A], ZA [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 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
  
• Version 1.1: 2024-11-13
  Changes: Data collection, Structure summary
• Version 1.2: 2025-01-15
  Changes: Data collection, Database references