8VKP

Cryo-EM structure of SARS-CoV-2 XBB.1.5 spike protein in complex with human ACE2 (focused refinement of RBD and ACE2)

• PDB DOI: https://doi.org/10.2210/pdb8VKP/pdb
• EM Map EMD-43325: EMDB EMDataResource

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2024-01-09 Released: 2024-02-14 
• Deposition Author(s): Zhu, X., Mannar, D., Saville, J., Poloni, C., Bezeruk, A., Tidey, K., Ahmed, S., Tuttle, K., Vahdatihassani, F., Cholak, S., Cook, L., Steiner, T.S., Subramaniam, S.
• Funding Organization(s): Canada Excellence Research Chair Award

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.77 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

SARS-CoV-2 XBB.1.5 Spike Protein: Altered Receptor Binding, Antibody Evasion, and Retention of T Cell Recognition

Mannar, D., Saville, J., Poloni, C., Zhu, X., Bezeruk, A., Tidey, K., Ahmed, S., Tuttle, K., Vahdatihassani, F., Cholak, S., Cook, L., Steiner, T.S., Subramaniam, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 94.92 kDa 
• Atom Count: 6,577 
• Modelled Residue Count: 796 
• Deposited Residue Count: 807 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A	201	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Processed angiotensin-converting enzyme 2	B [auth D]	606	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	C [auth B], D [auth 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	E [auth A], F [auth D], G [auth D], H [auth D], I [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.77 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-02-14 
Deposition Author(s): Zhu, X., Mannar, D., Saville, J., Poloni, C., Bezeruk, A., Tidey, K., Ahmed, S., Tuttle, K., Vahdatihassani, F., Cholak, S., Cook, L., Steiner, T.S., Subramaniam, S.

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Funding Organization	Location	Grant Number
Canada Excellence Research Chair Award	Canada	--

Revision History  

• Version 1.0: 2024-02-14
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Data collection, Structure summary