8IF2 | pdb_00008if2

Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron BQ.1.1 variant spike protein in complex with its receptor ACE2

• PDB DOI: https://doi.org/10.2210/pdb8IF2/pdb

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


• Deposited: 2023-02-17 Released: 2023-05-17 
• Deposition Author(s): Kimura, K., Suzuki, T., Hashiguchi, T.
• Funding Organization(s): Japan Science and Technology

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.78 Å
• R-Value Free: 
  0.245 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Convergent evolution of SARS-CoV-2 Omicron subvariants leading to the emergence of BQ.1.1 variant.

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

(2023) Nat Commun 14: 2671-2671

• PubMed: 37169744 
• DOI: https://doi.org/10.1038/s41467-023-38188-z
• Primary Citation of Related Structures:  
  8IF2


• PubMed Abstract: 
  

  In late 2022, various Omicron subvariants emerged and cocirculated worldwide. These variants convergently acquired amino acid substitutions at critical residues in the spike protein, including residues R346, K444, L452, N460, and F486. Here, we characterize the convergent evolution of Omicron subvariants and the properties of one recent lineage of concern, BQ.1.1. Our phylogenetic analysis suggests that these five substitutions are recurrently acquired, particularly in younger Omicron lineages. Epidemic dynamics modelling suggests that the five substitutions increase viral fitness, and a large proportion of the fitness variation within Omicron lineages can be explained by these substitutions. Compared to BA.5, BQ.1.1 evades breakthrough BA.2 and BA.5 infection sera more efficiently, as demonstrated by neutralization assays. The pathogenicity of BQ.1.1 in hamsters is lower than that of BA.5. Our multiscale investigations illuminate the evolutionary rules governing the convergent evolution for known Omicron lineages as of 2022.

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Organizational Affiliation: 
• Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan.
Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan.
Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.
First Medical Faculty at Biocev, Charles University, Vestec-Prague, Czechia.
Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan.
Center for iPS Cell Research and Application (CiRA), 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.
Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, UK.
Division of Risk Analysis and Management, International Institute for Zoonosis Control, 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.
Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan.
Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Japan.
Department of Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan.
Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan.
Division of International Research Promotion, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan.
One Health Research Center, Hokkaido University, Sapporo, Japan.
Institute for Vaccine Research and Development: HU-IVReD, Hokkaido University, Sapporo, Japan.
Tokyo Metropolitan Institute of Public Health, Tokyo, Japan.
HiLung, Inc, Kyoto, Japan.
Interpark Kuramochi Clinic, Utsunomiya, Japan.
Department of Global Health Promotion, Tokyo Medical and Dental University, Tokyo, Japan.
Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan.
International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan.
AMED-CREST, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan.
Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan. [e-mail].
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].
Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan. [e-mail].
AMED-CREST, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan. [e-mail].
Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Japan. [e-mail].
Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, 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].
International Vaccine Design Center, 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].
Collaboration Unit for Infection, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan. [e-mail].
CREST, Japan Science and Technology Agency, Kawaguchi, Japan. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 99.52 kDa 
• Atom Count: 6,713 
• Modeled Residue Count: 794 
• Deposited Residue Count: 832 
• Unique protein chains: 2

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 (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: 5		Go to GlyGen: Q9BYF1-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	B	224	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 20  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P0DTC2-1

Oligosaccharides

Help

Entity ID: 3
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	C [auth J], F [auth N], G [auth O]	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth K]	7		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G55220VL GlyCosmos:  G55220VL GlyGen:  G55220VL

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth L]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	I [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN (Subject of Investigation/LOI)	H [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.78 Å
• R-Value Free:  0.245 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 3₂ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.052	α = 90
b = 120.052	β = 90
c = 167.416	γ = 120

Software Package:

Software Name	Purpose
BUCCANEER	model building
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-05-17 
Deposition Author(s): Kimura, K., Suzuki, T., Hashiguchi, T.

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Funding Organization	Location	Grant Number
Japan Science and Technology	Japan	JPMJCR20H8

Revision History  

• Version 1.0: 2023-05-17
  Type: Initial release
  
• Version 1.1: 2023-05-24
  Changes: Database references
• Version 1.2: 2024-11-20
  Changes: Data collection, Structure summary