8I9F | pdb_00008i9f

S-RBD (Omicron BA.2.75) in complex with PD of ACE2

• PDB DOI: https://doi.org/10.2210/pdb8I9F/pdb
• EM Map EMD-35269: EMDB EMDataResource

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


• Deposited: 2023-02-06 Released: 2024-02-07 
• Deposition Author(s): Li, Y.N., Shen, Y.P., Zhang, Y.Y., Yan, R.H.
• Funding Organization(s): Ministry of Science and Technology (MoST, China)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structures of SARS-CoV-2 BA.2-derived subvariants spike in complex with ACE2 receptor.

Li, Y., Ren, C., Shen, Y., Zhang, Y., Chen, J., Zheng, J., Tian, R., Cao, L., Yan, R.

(2023) Cell Discov 9: 108-108

• PubMed: 37919275 
• DOI: https://doi.org/10.1038/s41421-023-00607-2
• Primary Citation of Related Structures:  
  8I9B, 8I9C, 8I9D, 8I9F, 8I9G, 8I9H

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Organizational Affiliation: 
• Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.
Department of Biochemistry, Key University Laboratory of Metabolism and Health of Guangdong, School of Medicine, Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, Guangdong, China.
Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, School of Science, Southern University of Science and Technology, Shenzhen, Guangdong, China.
Clinical Center for Molecular Diagnosis and Therapy, the Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian, China.
Department of Biochemistry, Key University Laboratory of Metabolism and Health of Guangdong, School of Medicine, Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, Guangdong, China. [e-mail].
Department of Biochemistry, Key University Laboratory of Metabolism and Health of Guangdong, School of Medicine, Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, Guangdong, China. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 99.14 kDa 
• Atom Count: 6,415 
• Modeled Residue Count: 764 
• Deposited Residue Count: 839 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Processed angiotensin-converting enzyme 2	A	616	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S2'	B [auth E]	223	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 17  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
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C [auth B], D [auth C], E [auth D], F, G, H	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)	I [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: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.0.6

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-02-07 
Deposition Author(s): Li, Y.N., Shen, Y.P., Zhang, Y.Y., Yan, R.H.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2020YFA0509301

Revision History  

• Version 1.0: 2024-02-07
  Type: Initial release
  
• Version 1.1: 2024-08-21
  Changes: Data collection, Database references
• Version 1.2: 2024-10-16
  Changes: Data collection, Structure summary