7S5Q | pdb_00007s5q

Crystal structure of SARS-CoV-2 B.1.351 variant receptor binding domain in complex with neutralizing antibodies CS44 and COVA1-16

PDB DOI: https://doi.org/10.2210/pdb7S5Q/pdb

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
Expression System: Trichoplusia ni, Mus musculus
Mutation(s): Yes

Deposited: 2021-09-11 Released: 2022-03-09
Deposition Author(s): Yuan, M., Wilson, I.A.
Funding Organization(s): Bill & Melinda Gates Foundation, Bavarian State Ministry for Education, Culture, Science and Arts

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.88 Å
R-Value Free:
0.257 (Depositor), 0.254 (DCC)
R-Value Work:
0.216 (Depositor), 0.213 (DCC)
R-Value Observed:
0.218 (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

SARS-CoV-2 Beta variant infection elicits potent lineage-specific and cross-reactive antibodies.

Reincke, S.M., Yuan, M., Kornau, H.C., Corman, V.M., van Hoof, S., Sanchez-Sendin, E., Ramberger, M., Yu, W., Hua, Y., Tien, H., Schmidt, M.L., Schwarz, T., Jeworowski, L.M., Brandl, S.E., Rasmussen, H.F., Homeyer, M.A., Stoffler, L., Barner, M., Kunkel, D., Huo, S., Horler, J., von Wardenburg, N., Kroidl, I., Eser, T.M., Wieser, A., Geldmacher, C., Hoelscher, M., Ganzer, H., Weiss, G., Schmitz, D., Drosten, C., Pruss, H., Wilson, I.A., Kreye, J.

(2022) Science 375: 782-787

PubMed: 35076281 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/science.abm5835
Primary Citation Related Structures:
7S5P, 7S5Q, 7S5R

PubMed Abstract:
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Beta variant of concern (VOC) resists neutralization by major classes of antibodies from COVID-19 patients and vaccinated individuals. In this study, serum of Beta-infected patients revealed reduced cross-neutralization of wild-type virus. From these patients, we isolated Beta-specific and cross-reactive receptor-binding domain (RBD) antibodies. The Beta-specificity results from recruitment of VOC-specific clonotypes and accommodation of mutations present in Beta and Omicron into a major antibody class that is normally sensitive to these mutations. The Beta-elicited cross-reactive antibodies share genetic and structural features with wild type-elicited antibodies, including a public VH1-58 clonotype that targets the RBD ridge. These findings advance our understanding of the antibody response to SARS-CoV-2 shaped by antigenic drift, with implications for design of next-generation vaccines and therapeutics.

Organizational Affiliation

Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.

Macromolecule Content

Total Structure Weight: 123.69 kDa
Atom Count: 8,323
Modeled Residue Count: 1,068
Deposited Residue Count: 1,118
Unique protein chains: 5

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A	231	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 3 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 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
CS44 Heavy chain	B	226	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CS44 Light chain	C	215	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
COVA1-16 Heavy chain	D [auth H]	232	Homo sapiens	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
COVA1-16 Light chain	E [auth L]	214	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth B] SDF format, chain Q [auth H] SDF format, chain R [auth H] SDF format, chain S [auth H] SDF format, chain V [auth L] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth H] MOL2 format, chain R [auth H] MOL2 format, chain S [auth H] MOL2 format, chain V [auth L] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth H] mmCIF format, chain R [auth H] mmCIF format, chain S [auth H] mmCIF format, chain V [auth L]	I [auth A] J [auth A] K [auth A] L [auth A] M [auth A] I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth B], Q [auth H], R [auth H], S [auth H], V [auth L]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain Q [auth H] Focus chain R [auth H] Focus chain S [auth H] Focus chain V [auth L] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain Q [auth H] Focus chain R [auth H] Focus chain S [auth H] Focus chain V [auth L]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain U [auth L] SDF format, chain T [auth L] SDF format, chain P [auth H] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain U [auth L] MOL2 format, chain T [auth L] MOL2 format, chain P [auth H] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain U [auth L] mmCIF format, chain T [auth L] mmCIF format, chain P [auth H] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A], P [auth H], T [auth L], U [auth L]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain P [auth H] Focus chain T [auth L] Focus chain U [auth L] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain P [auth H] Focus chain T [auth L] Focus chain U [auth L]