7PKI | pdb_00007pki

Crystal structure of human ACE2 bound to the spike receptor-binding domain from a cave bat sarbecovirus closely related to SARS-CoV-2.

• PDB DOI: https://doi.org/10.2210/pdb7PKI/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Homo sapiens, Sarbecovirus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2021-08-25 Released: 2022-01-19 
• Deposition Author(s): Baquero, E., Rey, F.A.
• Funding Organization(s): Pasteur Institute

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.94 Å
• R-Value Free: 
  0.227 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Starting Model: experimental

Literature

Bat coronaviruses related to SARS-CoV-2 and infectious for human cells.

Temmam, S., Vongphayloth, K., Baquero, E., Munier, S., Bonomi, M., Regnault, B., Douangboubpha, B., Karami, Y., Chretien, D., Sanamxay, D., Xayaphet, V., Paphaphanh, P., Lacoste, V., Somlor, S., Lakeomany, K., Phommavanh, N., Perot, P., Dehan, O., Amara, F., Donati, F., Bigot, T., Nilges, M., Rey, F.A., van der Werf, S., Brey, P.T., Eloit, M.

(2022) Nature 604: 330-336

• PubMed: 35172323 
• DOI: https://doi.org/10.1038/s41586-022-04532-4
• Primary Citation Related Structures: 
  7PKI


• PubMed Abstract: 
  

  The animal reservoir of SARS-CoV-2 is unknown despite reports of SARS-CoV-2-related viruses in Asian Rhinolophus bats ^1-4 , including the closest virus from R. affinis, RaTG13 (refs. ^5,6 ), and pangolins ^7-9 . SARS-CoV-2 has a mosaic genome, to which different progenitors contribute. The spike sequence determines the binding affinity and accessibility of its receptor-binding domain to the cellular angiotensin-converting enzyme 2 (ACE2) receptor and is responsible for host range ^10-12 . SARS-CoV-2 progenitor bat viruses genetically close to SARS-CoV-2 and able to enter human cells through a human ACE2 (hACE2) pathway have not yet been identified, although they would be key in understanding the origin of the epidemic. Here we show that such viruses circulate in cave bats living in the limestone karstic terrain in northern Laos, in the Indochinese peninsula. We found that the receptor-binding domains of these viruses differ from that of SARS-CoV-2 by only one or two residues at the interface with ACE2, bind more efficiently to the hACE2 protein than that of the SARS-CoV-2 strain isolated in Wuhan from early human cases, and mediate hACE2-dependent entry and replication in human cells, which is inhibited by antibodies that neutralize SARS-CoV-2. None of these bat viruses contains a furin cleavage site in the spike protein. Our findings therefore indicate that bat-borne SARS-CoV-2-like viruses that are potentially infectious for humans circulate in Rhinolophus spp. in the Indochinese peninsula.

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Organizational Affiliation: 
• Institut Pasteur, Université de Paris, Pathogen Discovery Laboratory, Paris, France.
Institut Pasteur, Université de Paris, The OIE Collaborating Center for the Detection and Identification in Humans of Emerging Animal Pathogens, Paris, France.
Institut Pasteur du Laos, Vientiane, Lao People's Democratic Republic.
Institut Pasteur, Université de Paris, CNRS UMR 3569, Structural Virology Unit, Paris, France.
Institut Pasteur, Université de Paris, CNRS UMR 3569, Molecular Genetics of RNA Viruses Unit, Paris, France.
Institut Pasteur, Université de Paris, CNRS UMR 3528, Structural Bioinformatics Unit, Paris, France.
Faculty of Environmental Sciences, National University of Laos, Vientiane, Lao People's Democratic Republic.
Institut Pasteur, Université de Paris, National Reference Center for Respiratory Viruses, Paris, France.
Institut Pasteur, Université de Paris, Bioinformatic and Biostatistic Hub - Computational Biology Department, Paris, France.
Institut Pasteur, Université de Paris, Pathogen Discovery Laboratory, Paris, France. [e-mail].
Institut Pasteur, Université de Paris, The OIE Collaborating Center for the Detection and Identification in Humans of Emerging Animal Pathogens, Paris, France. [e-mail].
Ecole Nationale Vétérinaire d'Alfort, University of Paris-Est, Maisons-Alfort, France. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 94.12 kDa 
• Atom Count: 6,610 
• Modeled Residue Count: 793 
• Deposited Residue Count: 793 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Processed angiotensin-converting enzyme 2	A	596	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: 5		Go to GlyGen: Q9BYF1-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BANAL 236 coronavirus spike receptor-binding domain	B [auth E]	197	Sarbecovirus	Mutation(s): 0  Gene Names: Spike
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: P0DTC2-1

Oligosaccharides

Help  

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C [auth B]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth A], E [auth A], F [auth A], G [auth A], O [auth E], P [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
TRS	K [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
PEG	L [auth A], M [auth A], T [auth E], U [auth E], V [auth E]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	H [auth A], I [auth A], J [auth A], Q [auth E]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	W [auth E]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	N [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	R [auth E], S [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.94 Å
• R-Value Free:  0.227 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 341.535	α = 90
b = 341.535	β = 90
c = 68.153	γ = 120

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-01-19 
Deposition Author(s): Baquero, E., Rey, F.A.

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Funding Organization	Location	Grant Number
Pasteur Institute	France	AlloSpike

Revision History  

• Version 1.0: 2022-01-19
  Type: Initial release
  
• Version 1.1: 2023-02-01
  Changes: Database references
• Version 1.2: 2024-02-07
  Changes: Data collection, Refinement description
• Version 1.3: 2024-10-09
  Changes: Structure summary