9BNE | pdb_00009bne

SARS-CoV-2 spike HexaPro protein in complex with T3A trimeric antagonist

PDB DOI: https://doi.org/10.2210/pdb9BNE/pdb
EM Map EMD-44725: EMDB EMDataResource

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

Deposited: 2024-05-02 Released: 2025-08-27
Deposition Author(s): Young, T.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.43 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Development of an ultrahigh affinity, trimeric ACE2 biologic as a universal SARS-CoV-2 antagonist.

Gonzales, J., Young, T., Choi, H., Park, M., Jewel, Y., Fan, C., Purohit, R., Bjorkman, P.J., Williams, J.C.

(2025) Commun Biol 8: 1428-1428

PubMed: 41053501 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s42003-025-08819-w
Primary Citation Related Structures:
9BNB, 9BNC, 9BND, 9BNE, 9BNF, 9BNG

PubMed Abstract:
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for the COVID-19 pandemic, utilizes membrane-bound, angiotensin-converting enzyme II (ACE2) for internalization and infection. We describe the development of a biologic that takes advantage of the proximity of the N-terminus of bound ACE2 to the three-fold symmetry axis of the spike protein to create an ultrapotent, trivalent ACE2 entry antagonist. Distinct disulfide bonds were added to enhance serum stability and a single point mutation was introduced to eliminate enzymatic activity. Through surface plasmon resonance, pseudovirus neutralization assays, and single-particle cryo-electron microscopy, we show this antagonist binds to and inhibits SARS-CoV-2 variants. We further show the antagonist binds to and inhibits a 2003 SARS-CoV-1 strain. Collectively, structural insight has allowed us to design a universal trivalent antagonist against all variants of SARS-CoV-2 tested, suggesting it will be active against the emergence of future mutants.

Organizational Affiliation

Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute, City of Hope, Duarte, CA, USA.

Macromolecule Content

Total Structure Weight: 675.37 kDa
Atom Count: 40,071
Modeled Residue Count: 4,955
Deposited Residue Count: 5,904
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Collagen alpha-1(XVIII) chain,Processed angiotensin-converting enzyme 2	A, C, E	680	Homo sapiens	Mutation(s): 0 Gene Names: COL18A1, ACE2, UNQ868/PRO1885 EC: 3.4.17 (UniProt), 3.4.17.23 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P39060 (Homo sapiens) Explore P39060 Go to UniProtKB: P39060
PHAROS: P39060 GTEx: ENSG00000182871
Find proteins for Q9BYF1 (Homo sapiens) Explore Q9BYF1 Go to UniProtKB: Q9BYF1
PHAROS: Q9BYF1 GTEx: ENSG00000130234
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	P39060 Q9BYF1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	B, D, F	1,288	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 9 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: 15	Glycosylation Focus chain B Focus chain D Focus chain F	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain GA [auth D] SDF format, chain LA [auth D] SDF format, chain MA [auth D] SDF format, chain NA [auth D] SDF format, chain OA [auth F] SDF format, chain PA [auth F] SDF format, chain RA [auth F] SDF format, chain S [auth B] SDF format, chain SA [auth F] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain UA [auth F] SDF format, chain VA [auth F] SDF format, chain W [auth B] SDF format, chain WA [auth F] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain YA [auth F] SDF format, chain Z [auth B] SDF format, chain XA [auth F] SDF format, chain V [auth B] SDF format, chain TA [auth F] SDF format, chain QA [auth F] SDF format, chain KA [auth D] SDF format, chain JA [auth D] SDF format, chain IA [auth D] SDF format, chain HA [auth D] SDF format, chain CA [auth D] SDF format, chain BA [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain LA [auth D] MOL2 format, chain MA [auth D] MOL2 format, chain NA [auth D] MOL2 format, chain OA [auth F] MOL2 format, chain PA [auth F] MOL2 format, chain RA [auth F] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth F] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth F] MOL2 format, chain VA [auth F] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth F] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain YA [auth F] MOL2 format, chain Z [auth B] MOL2 format, chain XA [auth F] MOL2 format, chain V [auth B] MOL2 format, chain TA [auth F] MOL2 format, chain QA [auth F] MOL2 format, chain KA [auth D] MOL2 format, chain JA [auth D] MOL2 format, chain IA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain BA [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain GA [auth D] mmCIF format, chain LA [auth D] mmCIF format, chain MA [auth D] mmCIF format, chain NA [auth D] mmCIF format, chain OA [auth F] mmCIF format, chain PA [auth F] mmCIF format, chain RA [auth F] mmCIF format, chain S [auth B] mmCIF format, chain SA [auth F] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain UA [auth F] mmCIF format, chain VA [auth F] mmCIF format, chain W [auth B] mmCIF format, chain WA [auth F] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain YA [auth F] mmCIF format, chain Z [auth B] mmCIF format, chain XA [auth F] mmCIF format, chain V [auth B] mmCIF format, chain TA [auth F] mmCIF format, chain QA [auth F] mmCIF format, chain KA [auth D] mmCIF format, chain JA [auth D] mmCIF format, chain IA [auth D] mmCIF format, chain HA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain BA [auth B]	AA [auth B] BA [auth B] CA [auth D] DA [auth D] EA [auth D] AA [auth B], BA [auth B], CA [auth D], DA [auth D], EA [auth D], FA [auth D], GA [auth D], HA [auth D], IA [auth D], JA [auth D], KA [auth D], LA [auth D], MA [auth D], NA [auth D], OA [auth F], PA [auth F], QA [auth F], RA [auth F], S [auth B], SA [auth F], T [auth B], TA [auth F], U [auth B], UA [auth F], V [auth B], VA [auth F], W [auth B], WA [auth F], X [auth B], XA [auth F], Y [auth B], YA [auth F], 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 D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain OA [auth F] Focus chain PA [auth F] Focus chain QA [auth F] Focus chain RA [auth F] Focus chain S [auth B] Focus chain SA [auth F] Focus chain T [auth B] Focus chain TA [auth F] Focus chain U [auth B] Focus chain UA [auth F] Focus chain V [auth B] Focus chain VA [auth F] Focus chain W [auth B] Focus chain WA [auth F] Focus chain X [auth B] Focus chain XA [auth F] Focus chain Y [auth B] Focus chain YA [auth F] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain OA [auth F] Focus chain PA [auth F] Focus chain QA [auth F] Focus chain RA [auth F] Focus chain S [auth B] Focus chain SA [auth F] Focus chain T [auth B] Focus chain TA [auth F] Focus chain U [auth B] Focus chain UA [auth F] Focus chain V [auth B] Focus chain VA [auth F] Focus chain W [auth B] Focus chain WA [auth F] Focus chain X [auth B] Focus chain XA [auth F] Focus chain Y [auth B] Focus chain YA [auth F] Focus chain Z [auth B]