7XBH | pdb_00007xbh

The complex structure of RshSTT182/200 RBD bound to human ACE2

• PDB DOI: https://doi.org/10.2210/pdb7XBH/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Rhinolophus shameli, Homo sapiens
• Expression System: Homo sapiens, Insect cell expression vector pTIE1
• Mutation(s): No 


• Deposited: 2022-03-21 Released: 2023-01-11 
• Deposition Author(s): Hu, Y., Liu, K.F., Han, P., Qi, J.X.
• Funding Organization(s): Chinese Academy of Sciences

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.02 Å
• R-Value Free: 
  0.235 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Host range and structural analysis of bat-origin RshSTT182/200 coronavirus binding to human ACE2 and its animal orthologs.

Hu, Y., Liu, K., Han, P., Xu, Z., Zheng, A., Pan, X., Jia, Y., Su, C., Tang, L., Wu, L., Bai, B., Zhao, X., Tian, D., Chen, Z., Qi, J., Wang, Q., Gao, G.F.

(2023) EMBO J 42: e111737-e111737

• PubMed: 36519268 
• DOI: https://doi.org/10.15252/embj.2022111737
• Primary Citation Related Structures: 
  7XBF, 7XBG, 7XBH


• PubMed Abstract: 
  

  Bat-origin RshSTT182 and RshSTT200 coronaviruses (CoV) from Rhinolophus shameli in Southeast Asia (Cambodia) share 92.6% whole-genome identity with SARS-CoV-2 and show identical receptor-binding domains (RBDs). In this study, we determined the structure of the RshSTT182/200 receptor binding domain (RBD) in complex with human angiotensin-converting enzyme 2 (hACE2) and identified the key residues that influence receptor binding. The binding of the RshSTT182/200 RBD to ACE2 orthologs from 39 animal species, including 18 bat species, was used to evaluate its host range. The RshSTT182/200 RBD broadly recognized 21 of 39 ACE2 orthologs, although its binding affinities for the orthologs were weaker than those of the RBD of SARS-CoV-2. Furthermore, RshSTT182 pseudovirus could utilize human, fox, and Rhinolophus affinis ACE2 receptors for cell entry. Moreover, we found that SARS-CoV-2 induces cross-neutralizing antibodies against RshSTT182 pseudovirus. Taken together, these findings indicate that RshSTT182/200 can potentially infect susceptible animals, but requires further evolution to obtain strong interspecies transmission abilities like SARS-CoV-2.

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Organizational Affiliation: 
• School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
Faculty of Health Sciences, University of Macau, Macau SAR, China.
University of Chinese Academy of Sciences, Beijing, China.
College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China.
Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China.
Center of Infectious Disease, Beijing Ditan Hospital, Capital Medical University, Beijing, China.

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: 95.49 kDa 
• Atom Count: 6,607 
• Modeled Residue Count: 806 
• Deposited Residue Count: 820 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RshSTT182/200 coronavirus receptor binding domain	A [auth B]	218	Rhinolophus shameli	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Processed angiotensin-converting enzyme 2	B [auth A]	602	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: 4		Go to GlyGen: Q9BYF1-1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	C [auth B], D [auth A], E [auth A], F [auth A], G [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: 3.02 Å
• R-Value Free:  0.235 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 155.413	α = 90
b = 155.229	β = 103.661
c = 60.996	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-01-11 
Deposition Author(s): Hu, Y., Liu, K.F., Han, P., Qi, J.X.

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Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	XDB29010202

Revision History  

• Version 1.0: 2023-01-11
  Type: Initial release
  
• Version 1.1: 2023-03-01
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.3: 2024-10-30
  Changes: Structure summary