8XN3

SARS-CoV-2 Omicron HV.1 RBD in complex with human ACE2 (local refinement from the spike protein)

• PDB DOI: https://doi.org/10.2210/pdb8XN3/pdb
• EM Map EMD-38496: EMDB EMDataResource

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


• Deposited: 2023-12-28 Released: 2024-07-03 
• Deposition Author(s): Li, L.J., Gu, Y.H., Shi, K.Y., Qi, J.X., Gao, G.F.
• Funding Organization(s): Chinese Academy of Sciences

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.64 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis of receptor binding and immune escape for SARS-CoV-2 Omicron BA.2.86, EG.5, EG.5.1 and HV.1 sub-variants

Li, L.J., Xu, Z.P., Liu, K.F., Gao, G.F.

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: 96.54 kDa 
• Atom Count: 6,505 
• Modelled Residue Count: 791 
• Deposited Residue Count: 826 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Angiotensin-converting enzyme 2	A	603	Homo sapiens	Mutation(s): 0  Gene Names: ACE2, UNQ868/PRO1885 EC: 3.4.17.23 (PDB Primary Data), 3.4.17 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYF1 (Homo sapiens) Explore Q9BYF1  Go to UniProtKB:  Q9BYF1
GTEx:  ENSG00000130234
Glycosylation
Glycosylation Sites: 6		Go to GlyGen: Q9BYF1-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	B	223	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 24  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.64 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-03 
Deposition Author(s): Li, L.J., Gu, Y.H., Shi, K.Y., Qi, J.X., Gao, G.F.

---

Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	XDB29010202

Revision History  

• Version 1.0: 2024-07-03
  Type: Initial release