8YF2 | pdb_00008yf2

Cryo-EM structure of SARS-CoV-2 prototype RBD in complex with raccoon dog ACE2 (local refinement)

• PDB DOI: https://doi.org/10.2210/pdb8YF2/pdb
• EM Map EMD-39208: EMDB EMDataResource

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


• Deposited: 2024-02-23 Released: 2024-10-23 
• Deposition Author(s): Li, L.J., Luo, C.L., Qi, J.X., Gao, G.F.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

---

Experimental Data Snapshot

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

Literature

Receptor binding and structural basis of raccoon dog ACE2 binding to SARS-CoV-2 prototype and its variants.

Luo, C., Li, L., Gu, Y., Zhang, H., Xu, Z., Sun, J., Shi, K., Ma, S., Tian, W.X., Liu, K., Gao, G.F.

(2024) PLoS Pathog 20: e1012713-e1012713

• PubMed: 39637248 
• DOI: https://doi.org/10.1371/journal.ppat.1012713
• Primary Citation of Related Structures:  
  8YF2, 8YFT


• PubMed Abstract: 
  

  Raccoon dog was proposed as a potential host of SARS-CoV-2, but no evidence support such a notion. In our study, we investigated the binding affinities of raccoon dog ACE2 (rdACE2) to the spike (S) protein receptor binding domain (RBD) of SARS-CoV-2 prototype (PT) and its variants. It revealed that the binding affinities of RBD from SARS-CoV-2 variants were generally lower than that of the PT RBD. Through structural and functional analyses, we found amino acids H34 and M82 play pivotal roles in maintaining the binding affinity of ACE2 to different SARS-CoV-2 sub-variants. These results suggest that raccoon dogs exhibit lower susceptibility to SARS-CoV-2 compared to those animal species with a high prevalence of SARS-CoV-2 transmission.

---

Organizational Affiliation: 
• College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China.
CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China.
Beijing Life Science Academy, Beijing, China.
School of Life Sciences, Yunnan University, Kunming, China.
Faculty of Health Sciences, University of Macau, Macau SAR, China.
Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, China.

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: 98.54 kDa 
• Atom Count: 6,504 
• Modeled Residue Count: 783 
• Deposited Residue Count: 834 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A [auth B]	229	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
Angiotensin-converting enzyme	B [auth A]	605	Nyctereutes procyonoides	Mutation(s): 0  Gene Names: ACE2, NYPRO_LOCUS14582 EC: 3.4
UniProt
Find proteins for B4XEP4 (Nyctereutes procyonoides) Explore B4XEP4  Go to UniProtKB:  B4XEP4
Glycosylation
Glycosylation Sites: 4

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, D, E, F	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)	H [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN (Subject of Investigation/LOI)	G [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: 2024-10-23 
Deposition Author(s): Li, L.J., Luo, C.L., Qi, J.X., Gao, G.F.

---

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2024-10-23
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection
• Version 1.2: 2025-04-30
  Changes: Data collection, Database references