7U2E | pdb_00007u2e

Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody ADI-55688

PDB DOI: https://doi.org/10.2210/pdb7U2E/pdb

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
Expression System: Trichoplusia ni, Mus musculus
Mutation(s): No

Deposited: 2022-02-23 Released: 2022-05-04
Deposition Author(s): Yuan, M., Zhu, X., Wilson, I.A.
Funding Organization(s): Bill & Melinda Gates Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free:
0.284 (Depositor), 0.279 (DCC)
R-Value Work:
0.254 (Depositor), 0.254 (DCC)
R-Value Observed:
0.257 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

A broad and potent neutralization epitope in SARS-related coronaviruses.

Yuan, M., Zhu, X., He, W.T., Zhou, P., Kaku, C.I., Capozzola, T., Zhu, C.Y., Yu, X., Liu, H., Yu, W., Hua, Y., Tien, H., Peng, L., Song, G., Cottrell, C.A., Schief, W.R., Nemazee, D., Walker, L.M., Andrabi, R., Burton, D.R., Wilson, I.A.

(2022) Proc Natl Acad Sci U S A 119: e2205784119-e2205784119

PubMed: 35767670 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.2205784119
Primary Citation Related Structures:
7U2D, 7U2E

PubMed Abstract:
Many neutralizing antibodies (nAbs) elicited to ancestral severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) through natural infection and vaccination have reduced effectiveness to SARS-CoV-2 variants. Here, we show that therapeutic antibody ADG20 is able to neutralize SARS-CoV-2 variants of concern (VOCs) including Omicron (B.1.1.529) as well as other SARS-related coronaviruses. We delineate the structural basis of this relatively escape-resistant epitope that extends from one end of the receptor binding site (RBS) into the highly conserved CR3022 site. ADG20 can then benefit from high potency through direct competition with ACE2 in the more variable RBS and interaction with the more highly conserved CR3022 site. Importantly, antibodies that are able to target this site generally neutralize a broad range of VOCs, albeit with reduced potency against Omicron. Thus, this conserved and vulnerable site can be exploited for the design of universal vaccines and therapeutic antibodies.

Organizational Affiliation

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037.

Macromolecule Content

Total Structure Weight: 71.13 kDa
Atom Count: 4,835
Modeled Residue Count: 628
Deposited Residue Count: 650
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A	205	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0
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 A	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ADI-55688 heavy chain	B [auth H]	227	Homo sapiens	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ADI-55688 light chain	C [auth L]	218	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain M [auth L] SDF format, chain L SDF format, chain K [auth L] SDF format, chain J [auth H] SDF format, chain I [auth H] SDF format, chain H SDF format, chain G [auth H] SDF format, chain F [auth H] SDF format, chain E [auth A] MOL2 format, chain M [auth L] MOL2 format, chain L MOL2 format, chain K [auth L] MOL2 format, chain J [auth H] MOL2 format, chain I [auth H] MOL2 format, chain H MOL2 format, chain G [auth H] MOL2 format, chain F [auth H] MOL2 format, chain E [auth A] mmCIF format, chain M [auth L] mmCIF format, chain L mmCIF format, chain K [auth L] mmCIF format, chain J [auth H] mmCIF format, chain I [auth H] mmCIF format, chain H mmCIF format, chain G [auth H] mmCIF format, chain F [auth H] mmCIF format, chain E [auth A]	E [auth A] F [auth H] G [auth H] H I [auth H] E [auth A], F [auth H], G [auth H], H, I [auth H], J [auth H], K [auth L], L, M [auth L]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth H] Focus chain G [auth H] Focus chain H Focus chain I [auth H] Focus chain J [auth H] Focus chain K [auth L] Focus chain L Focus chain M [auth L] Interactions & Density Focus chain E [auth A] Focus chain F [auth H] Focus chain G [auth H] Focus chain H Focus chain I [auth H] Focus chain J [auth H] Focus chain K [auth L] Focus chain L Focus chain M [auth L]