7XA7 | pdb_00007xa7

Crystal structure of SARS-CoV-2 receptor-binding domain in complex with intermediate horseshoe bat ACE2

PDB DOI: https://doi.org/10.2210/pdb7XA7/pdb

Classification: VIRAL PROTEIN
Organism(s): Rhinolophus affinis, Severe acute respiratory syndrome coronavirus 2
Expression System: Escherichia coli, Homo sapiens
Mutation(s): No

Deposited: 2022-03-17 Released: 2022-12-21
Deposition Author(s): Tang, L.F., Zhang, D., Han, P., Qi, J.X.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.31 Å
R-Value Free:
0.254 (Depositor), 0.234 (DCC)
R-Value Work:
0.233 (Depositor)
R-Value Observed:
0.233 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structural basis of SARS-CoV-2 and its variants binding to intermediate horseshoe bat ACE2.

Tang, L., Zhang, D., Han, P., Kang, X., Zheng, A., Xu, Z., Zhao, X., Wang, V.Y., Qi, J., Wang, Q., Liu, K., Gao, G.F.

(2022) Int J Biol Sci 18: 4658-4668

PubMed: 35874946 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.7150/ijbs.73640
Primary Citation Related Structures:
7XA7

PubMed Abstract:
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused a global pandemic. Intermediate horseshoe bats ( Rhinolophus affinis ) are hosts of RaTG13, the second most phylogenetically related viruses to SARS-CoV-2. We report the binding between intermediate horseshoe bat ACE2 (bACE2-Ra) and SARS-CoV-2 receptor-binding domain (RBD), supporting the pseudotyped SARS-CoV-2 viral infection. A 3.3 Å resolution crystal structure of the bACE2-Ra/SARS-CoV-2 RBD complex was determined. The interaction networks of Patch 1 showed differences in R34 and E35 of bACE2-Ra compared to hACE2 and big-eared horseshoe bat ACE2 (bACE2-Rm). The E35K substitution, existing in other species, significantly enhanced the binding affinity owing to its electrostatic attraction with E484 of SARS-CoV-2 RBD. Furthermore, bACE2-Ra showed extensive support for the SARS-CoV-2 variants. These results broaden our knowledge of the ACE2/RBD interaction mechanism and emphasize the importance of continued surveillance of intermediate horseshoe bats to prevent spillover risk.

Organizational Affiliation

CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.

Macromolecule Content

Total Structure Weight: 380.49 kDa
Atom Count: 25,842
Modeled Residue Count: 3,164
Deposited Residue Count: 3,284
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Angiotensin-converting enzyme	A, C, E, G	598	Rhinolophus affinis	Mutation(s): 0 EC: 3.4
UniProt
Find proteins for A0A7D7FA76 (Rhinolophus affinis) Explore A0A7D7FA76 Go to UniProtKB: A0A7D7FA76
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A7D7FA76
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	B, D, F, H	223	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTC2
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B Focus chain D Focus chain F Focus chain H	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain P [auth H] SDF format, chain N [auth F] SDF format, chain J [auth B] MOL2 format, chain L [auth D] MOL2 format, chain P [auth H] MOL2 format, chain N [auth F] MOL2 format, chain J [auth B] mmCIF format, chain L [auth D] mmCIF format, chain P [auth H] mmCIF format, chain N [auth F] mmCIF format, chain J [auth B]	J [auth B], L [auth D], N [auth F], P [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain J [auth B] Focus chain L [auth D] Focus chain N [auth F] Focus chain P [auth H] Interactions & Density Focus chain J [auth B] Focus chain L [auth D] Focus chain N [auth F] Focus chain P [auth H]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain O [auth G] SDF format, chain M [auth E] SDF format, chain K [auth C] SDF format, chain I [auth A] MOL2 format, chain O [auth G] MOL2 format, chain M [auth E] MOL2 format, chain K [auth C] MOL2 format, chain I [auth A] mmCIF format, chain O [auth G] mmCIF format, chain M [auth E] mmCIF format, chain K [auth C] mmCIF format, chain I [auth A]	I [auth A], K [auth C], M [auth E], O [auth G]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain K [auth C] Focus chain M [auth E] Focus chain O [auth G] Interactions & Density Focus chain I [auth A] Focus chain K [auth C] Focus chain M [auth E] Focus chain O [auth G]