8BON | pdb_00008bon

Structure of the SARS-CoV-2 spike glycoprotein in complex with the macrocyclic peptide S1B3inL1

PDB DOI: https://doi.org/10.2210/pdb8BON/pdb
EM Map EMD-16144: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus 2, Tequatrovirus T4, synthetic construct
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2022-11-15 Released: 2023-06-28
Deposition Author(s): Hurdiss, D.L.
Funding Organization(s): Innovative Medicines Initiative

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

A broad-spectrum macrocyclic peptide inhibitor of the SARS-CoV-2 spike protein.

Thijssen, V., Hurdiss, D.L., Debski-Antoniak, O.J., Spence, M.A., Franck, C., Norman, A., Aggarwal, A., Mokiem, N.J., van Dongen, D.A.A., Vermeir, S.W., Liu, M., Li, W., Chatziandreou, M., Donselaar, T., Du, W., Drulyte, I., Bosch, B.J., Snijder, J., Turville, S.G., Payne, R.J., Jackson, C.J., van Kuppeveld, F.J.M., Jongkees, S.A.K.

(2023) Proc Natl Acad Sci U S A 120: e2303292120-e2303292120

PubMed: 37339194 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.2303292120
Primary Citation Related Structures:
8BON

PubMed Abstract:
The ongoing COVID-19 pandemic has had great societal and health consequences. Despite the availability of vaccines, infection rates remain high due to immune evasive Omicron sublineages. Broad-spectrum antivirals are needed to safeguard against emerging variants and future pandemics. We used messenger RNA (mRNA) display under a reprogrammed genetic code to find a spike-targeting macrocyclic peptide that inhibits SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) Wuhan strain infection and pseudoviruses containing spike proteins of SARS-CoV-2 variants or related sarbecoviruses. Structural and bioinformatic analyses reveal a conserved binding pocket between the receptor-binding domain, N-terminal domain, and S2 region, distal to the angiotensin-converting enzyme 2 receptor-interaction site. Our data reveal a hitherto unexplored site of vulnerability in sarbecoviruses that peptides and potentially other drug-like molecules can target.

Organizational Affiliation

Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht 3584 CG, the Netherlands.

Macromolecule Content

Total Structure Weight: 440.51 kDa
Atom Count: 25,930
Modeled Residue Count: 3,249
Deposited Residue Count: 3,882
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein,Fibritin	A [auth B], D [auth A], E [auth C]	1,275	Severe acute respiratory syndrome coronavirus 2, Tequatrovirus T4 This entity is chimeric	Mutation(s): 9 Gene Names: S, 2, wac
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2 Go to UniProtKB: P0DTC2
Find proteins for P10104 (Enterobacteria phage T4) Explore P10104 Go to UniProtKB: P10104
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	P0DTC2 P10104
Glycosylation
Glycosylation Sites: 13	Glycosylation Focus chain A [auth B] Focus chain D [auth A] Focus chain E [auth C]	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Macrocyclic peptide S1B3inL1	B [auth E], C [auth D], F	19	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

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	G, H, I, J, K G, H, I, J, K, L, M, N, O, P, Q, R, S	2		N-Glycosylation	Interactions Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Focus chain N Focus chain O Focus chain P Focus chain Q Focus chain R Focus chain S Interactions & Density Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Focus chain N Focus chain O Focus chain P Focus chain Q Focus chain R Focus chain S
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 Z [auth A] SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain PA [auth C] SDF format, chain OA [auth C] SDF format, chain NA [auth C] SDF format, chain MA [auth C] SDF format, chain LA [auth C] SDF format, chain KA [auth C] SDF format, chain JA [auth C] SDF format, chain IA [auth C] SDF format, chain HA [auth C] SDF format, chain GA [auth A] SDF format, chain FA [auth A] SDF format, chain EA [auth A] SDF format, chain DA [auth A] SDF format, chain CA [auth A] SDF format, chain BA [auth A] SDF format, chain AA [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain PA [auth C] MOL2 format, chain OA [auth C] MOL2 format, chain NA [auth C] MOL2 format, chain MA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain KA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain GA [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain AA [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain PA [auth C] mmCIF format, chain OA [auth C] mmCIF format, chain NA [auth C] mmCIF format, chain MA [auth C] mmCIF format, chain LA [auth C] mmCIF format, chain KA [auth C] mmCIF format, chain JA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain GA [auth A] mmCIF format, chain FA [auth A] mmCIF format, chain EA [auth A] mmCIF format, chain DA [auth A] mmCIF format, chain CA [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain AA [auth A]	AA [auth A] BA [auth A] CA [auth A] DA [auth A] EA [auth A] AA [auth A], BA [auth A], CA [auth A], DA [auth A], EA [auth A], FA [auth A], GA [auth A], HA [auth C], IA [auth C], JA [auth C], KA [auth C], LA [auth C], MA [auth C], NA [auth C], OA [auth C], PA [auth C], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth A]