8IFY | pdb_00008ify

Cryo-EM structure of SARS-CoV-2 Omicron BA.4/5 spike protein in complex with white-tailed deer ACE2

PDB DOI: https://doi.org/10.2210/pdb8IFY/pdb
EM Map EMD-35426: EMDB EMDataResource

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

Deposited: 2023-02-20 Released: 2023-08-30
Deposition Author(s): Han, P., Meng, Y.M., Qi, J.X.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.55 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structural basis of white-tailed deer, Odocoileus virginianus , ACE2 recognizing all the SARS-CoV-2 variants of concern with high affinity.

Han, P., Meng, Y., Zhang, D., Xu, Z., Li, Z., Pan, X., Zhao, Z., Li, L., Tang, L., Qi, J., Liu, K., Gao, G.F.

(2023) J Virol 97: e0050523-e0050523

PubMed: 37676003 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1128/jvi.00505-23
Primary Citation Related Structures:
8HFX, 8HFY, 8HFZ, 8HG0, 8IFY, 8IFZ

PubMed Abstract:
SARS-CoV-2 has been expanding its host range, among which the white-tailed deer (WTD), Odocoileus virginianus, became the first wildlife species infected on a large scale and might serve as a host reservoir for variants of concern (VOCs) in case no longer circulating in humans. In this study, we comprehensively assessed the binding of the WTD angiotensin-converting enzyme 2 (ACE2) receptor to the spike (S) receptor-binding domains (RBDs) from the SARS-CoV-2 prototype (PT) strain and multiple variants. We found that WTD ACE2 could be broadly recognized by all of the tested RBDs. We further determined the complex structures of WTD ACE2 with PT, Omicron BA.1, and BA.4/5 S trimer. Detailed structural comparison revealed the important roles of RBD residues on 486, 498, and 501 sites for WTD ACE2 binding. This study deepens our understanding of the interspecies transmission mechanisms of SARS-CoV-2 and further addresses the importance of constant monitoring on SARS-CoV-2 infections in wild animals. IMPORTANCE Even if we manage to eliminate the virus among humans, it will still circulate among wildlife and continuously be transmitted back to humans. A recent study indicated that WTD may serve as reservoir for nearly extinct SARS-CoV-2 strains. Therefore, it is critical to evaluate the binding abilities of SARS-CoV-2 variants to the WTD ACE2 receptor and elucidate the molecular mechanisms of binding of the RBDs to assess the risk of spillback events.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 540.11 kDa
Atom Count: 34,248
Modeled Residue Count: 4,218
Deposited Residue Count: 4,703
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1,127	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 33 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: 6	Glycosylation Focus chain A Focus chain B Focus chain C	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Angiotensin-converting enzyme	D [auth E], E [auth F]	661	Odocoileus virginianus	Mutation(s): 0 Gene Names: ACE2

Oligosaccharides

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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	F [auth G], G [auth H], H [auth I], I [auth J], J [auth K], F [auth G], G [auth H], H [auth I], I [auth J], J [auth K], K [auth L], L [auth N], M [auth O], N [auth P], O [auth Q], P [auth R], Q [auth S], R [auth T], S [auth U]	2		N/A	Interactions Focus chain F [auth G] Focus chain G [auth H] Focus chain H [auth I] Focus chain I [auth J] Focus chain J [auth K] Focus chain K [auth L] Focus chain L [auth N] Focus chain M [auth O] Focus chain N [auth P] Focus chain O [auth Q] Focus chain P [auth R] Focus chain Q [auth S] Focus chain R [auth T] Focus chain S [auth U] Interactions & Density Focus chain F [auth G] Focus chain G [auth H] Focus chain H [auth I] Focus chain I [auth J] Focus chain J [auth K] Focus chain K [auth L] Focus chain L [auth N] Focus chain M [auth O] Focus chain N [auth P] Focus chain O [auth Q] Focus chain P [auth R] Focus chain Q [auth S] Focus chain R [auth T] Focus chain S [auth U]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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 Z [auth B] SDF format, chain Y [auth B] SDF format, chain X [auth A] SDF format, chain W [auth A] SDF format, chain V [auth A] SDF format, chain U [auth A] SDF format, chain T [auth A] SDF format, chain SA [auth F] SDF format, chain RA [auth F] SDF format, chain QA [auth F] SDF format, chain PA [auth F] SDF format, chain OA [auth F] SDF format, chain MA [auth E] SDF format, chain LA [auth E] SDF format, chain KA [auth E] SDF format, chain JA [auth E] SDF format, chain IA [auth C] SDF format, chain HA [auth C] SDF format, chain GA [auth C] SDF format, chain FA [auth C] SDF format, chain EA [auth C] SDF format, chain DA [auth C] SDF format, chain CA [auth B] SDF format, chain BA [auth B] SDF format, chain AA [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth A] MOL2 format, chain W [auth A] MOL2 format, chain V [auth A] MOL2 format, chain U [auth A] MOL2 format, chain T [auth A] MOL2 format, chain SA [auth F] MOL2 format, chain RA [auth F] MOL2 format, chain QA [auth F] MOL2 format, chain PA [auth F] MOL2 format, chain OA [auth F] MOL2 format, chain MA [auth E] MOL2 format, chain LA [auth E] MOL2 format, chain KA [auth E] MOL2 format, chain JA [auth E] MOL2 format, chain IA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain CA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth A] mmCIF format, chain W [auth A] mmCIF format, chain V [auth A] mmCIF format, chain U [auth A] mmCIF format, chain T [auth A] mmCIF format, chain SA [auth F] mmCIF format, chain RA [auth F] mmCIF format, chain QA [auth F] mmCIF format, chain PA [auth F] mmCIF format, chain OA [auth F] mmCIF format, chain MA [auth E] mmCIF format, chain LA [auth E] mmCIF format, chain KA [auth E] mmCIF format, chain JA [auth E] mmCIF format, chain IA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain CA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain AA [auth B]	AA [auth B] BA [auth B] CA [auth B] DA [auth C] EA [auth C] AA [auth B], BA [auth B], CA [auth B], DA [auth C], EA [auth C], FA [auth C], GA [auth C], HA [auth C], IA [auth C], JA [auth E], KA [auth E], LA [auth E], MA [auth E], OA [auth F], PA [auth F], QA [auth F], RA [auth F], SA [auth F], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth B], Z [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain LA [auth E] Focus chain MA [auth E] Focus chain OA [auth F] Focus chain PA [auth F] Focus chain QA [auth F] Focus chain RA [auth F] Focus chain SA [auth F] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain LA [auth E] Focus chain MA [auth E] Focus chain OA [auth F] Focus chain PA [auth F] Focus chain QA [auth F] Focus chain RA [auth F] Focus chain SA [auth F] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth B] Focus chain Z [auth B]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain TA [auth F] SDF format, chain NA [auth E] MOL2 format, chain TA [auth F] MOL2 format, chain NA [auth E] mmCIF format, chain TA [auth F] mmCIF format, chain NA [auth E]	NA [auth E], TA [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain NA [auth E] Focus chain TA [auth F] Interactions & Density Focus chain NA [auth E] Focus chain TA [auth F]