7TCQ | pdb_00007tcq

Crystal structure of SARS-CoV-2 neutralizing antibody WS6 in complex with spike S2 peptide

PDB DOI: https://doi.org/10.2210/pdb7TCQ/pdb

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

Deposited: 2021-12-28 Released: 2022-08-03
Deposition Author(s): Zhou, T., Kwong, P.D.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free:
0.213 (Depositor), 0.213 (DCC)
R-Value Work:
0.172 (Depositor), 0.172 (DCC)
R-Value Observed:
0.172 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Vaccine-elicited murine antibody WS6 neutralizes diverse beta-coronaviruses by recognizing a helical stem supersite of vulnerability.

Shi, W., Wang, L., Zhou, T., Sastry, M., Yang, E.S., Zhang, Y., Chen, M., Chen, X., Choe, M., Creanga, A., Leung, K., Olia, A.S., Pegu, A., Rawi, R., Schon, A., Shen, C.H., Stancofski, E.D., Talana, C.A., Teng, I.T., Wang, S., Corbett, K.S., Tsybovsky, Y., Mascola, J.R., Kwong, P.D.

(2022) Structure 30: 1233

PubMed: 35841885 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.str.2022.06.004
Primary Citation Related Structures:
7TCQ

PubMed Abstract:
Immunization with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike elicits diverse antibodies, but it is unclear if any of the antibodies can neutralize broadly against other beta-coronaviruses. Here, we report antibody WS6 from a mouse immunized with mRNA encoding the SARS-CoV-2 spike. WS6 bound diverse beta-coronavirus spikes and neutralized SARS-CoV-2 variants, SARS-CoV, and related sarbecoviruses. Epitope mapping revealed WS6 to target a region in the S2 subunit, which was conserved among SARS-CoV-2, Middle East respiratory syndrome (MERS)-CoV, and hCoV-OC43. The crystal structure at 2 Å resolution of WS6 revealed recognition to center on a conserved S2 helix, which was occluded in both pre- and post-fusion spike conformations. Structural and neutralization analyses indicated WS6 to neutralize by inhibiting fusion and post-viral attachment. Comparison of WS6 with other recently identified antibodies that broadly neutralize beta-coronaviruses indicated a stem-helical supersite-centered on hydrophobic residues Phe1148, Leu1152, Tyr1155, and Phe1156-to be a promising target for vaccine design.

Organizational Affiliation

Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.

Macromolecule Content

Total Structure Weight: 97.94 kDa
Atom Count: 7,587
Modeled Residue Count: 877
Deposited Residue Count: 880
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-SARS-CoV-2 antibody WS6 Fab heavy chain	A [auth H], D [auth A]	216	Mus musculus	Mutation(s): 0

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-SARS-CoV-2 antibody WS6 Fab light chain	B [auth L]	212	Mus musculus	Mutation(s): 0

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Pegylated spike S2 peptide	C, F [auth D]	12	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1
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
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-SARS-CoV-2 antibody WS6 Fab light chain	E [auth B]	212	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain Q [auth L] SDF format, chain S [auth C] MOL2 format, chain Q [auth L] MOL2 format, chain S [auth C] mmCIF format, chain Q [auth L] mmCIF format, chain S [auth C]	Q [auth L], S [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain Q [auth L] Focus chain S [auth C] Interactions & Density Focus chain Q [auth L] Focus chain S [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain G [auth H] SDF format, chain H SDF format, chain I [auth H] SDF format, chain K [auth H] SDF format, chain L [auth H] SDF format, chain N [auth L] SDF format, chain O [auth L] SDF format, chain P [auth L] SDF format, chain R [auth C] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain Y [auth A] SDF format, chain Z [auth A] SDF format, chain V [auth A] SDF format, chain M [auth H] SDF format, chain J [auth H] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain G [auth H] MOL2 format, chain H MOL2 format, chain I [auth H] MOL2 format, chain K [auth H] MOL2 format, chain L [auth H] MOL2 format, chain N [auth L] MOL2 format, chain O [auth L] MOL2 format, chain P [auth L] MOL2 format, chain R [auth C] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain V [auth A] MOL2 format, chain M [auth H] MOL2 format, chain J [auth H] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain G [auth H] mmCIF format, chain H mmCIF format, chain I [auth H] mmCIF format, chain K [auth H] mmCIF format, chain L [auth H] mmCIF format, chain N [auth L] mmCIF format, chain O [auth L] mmCIF format, chain P [auth L] mmCIF format, chain R [auth C] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain W [auth A] mmCIF format, chain X [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain V [auth A] mmCIF format, chain M [auth H] mmCIF format, chain J [auth H]	AA [auth B] BA [auth B] G [auth H] H I [auth H] AA [auth B], BA [auth B], G [auth H], H, I [auth H], J [auth H], K [auth H], L [auth H], M [auth H], N [auth L], O [auth L], P [auth L], R [auth C], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain G [auth H] Focus chain H Focus chain I [auth H] Focus chain J [auth H] Focus chain K [auth H] Focus chain L [auth H] Focus chain M [auth H] Focus chain N [auth L] Focus chain O [auth L] Focus chain P [auth L] Focus chain R [auth C] 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 A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain G [auth H] Focus chain H Focus chain I [auth H] Focus chain J [auth H] Focus chain K [auth H] Focus chain L [auth H] Focus chain M [auth H] Focus chain N [auth L] Focus chain O [auth L] Focus chain P [auth L] Focus chain R [auth C] 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 A] Focus chain Z [auth A]