7WO5 | pdb_00007wo5

SARS-CoV-2 Spike in complex with IgG 553-15 (S-553-15 trimer)

PDB DOI: https://doi.org/10.2210/pdb7WO5/pdb
EM Map EMD-32639: EMDB EMDataResource

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

Deposited: 2022-01-20 Released: 2022-07-20
Deposition Author(s): Zhan, W.Q., Zhang, X., Chen, Z.G., Sun, L.
Funding Organization(s): Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.45 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Structural Study of SARS-CoV-2 Antibodies Identifies a Broad-Spectrum Antibody That Neutralizes the Omicron Variant by Disassembling the Spike Trimer.

Zhan, W., Tian, X., Zhang, X., Xing, S., Song, W., Liu, Q., Hao, A., Hu, Y., Zhang, M., Ying, T., Chen, Z., Lan, F., Sun, L.

(2022) J Virol 96: e0048022-e0048022

PubMed: 35924918 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1128/jvi.00480-22
Primary Citation Related Structures:
7WO4, 7WO5, 7WO7, 7WOA, 7WOB, 7WOC, 7WOG, 7WZ1, 7WZ2

PubMed Abstract:
The continuous emergence of novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants poses new challenges in the fight against the coronavirus disease 2019 (COVID-19) pandemic. The newly emerging Omicron strain caused serious immune escape and raised unprecedented concern all over the world. The development of an antibody targeting a conserved and universal epitope is urgently needed. A subset of neutralizing antibodies (NAbs) against COVID-19 from convalescent patients were isolated in our previous study. In this study, we investigated the accommodation of these NAbs to SARS-CoV-2 variants of concern (VOCs), revealing that IgG 553-49 neutralizes pseudovirus of the SARS-CoV-2 Omicron variant. In addition, we determined the cryo-electron microscopy (cryo-EM) structure of the SARS-CoV-2 spike (S) protein complexed with three monoclonal antibodies targeting different epitopes, including 553-49, 553-15, and 553-60. Notably, 553-49 targets a novel conserved epitope and neutralizes the virus by disassembling S trimers. IgG 553-15, an antibody that neutralizes all of the VOCs except Omicron, cross-links two S trimers to form a trimer dimer, demonstrating that 553-15 neutralizes the virus by steric hindrance and virion aggregation. These findings suggest the potential to develop 553-49 and other antibodies targeting this highly conserved epitope as promising therapeutic reagents for COVID-19. IMPORTANCE The emergence of the Omicron strain of SARS-CoV-2 caused higher immune escape, raising unprecedented concerns about the effectiveness of antibody therapies and vaccines. In this study, we identified a SARS-CoV-2 neutralizing antibody, 553-49, which neutralizes all variants by targeting a completely conserved novel epitope. In addition, we revealed that IgG 553-15 neutralizes SARS-CoV-2 by cross-linking virions and that 553-60 functions by blocking receptor binding. Comparison of different receptor binding domain (RBD) epitopes revealed that the 553-49 epitope is hidden in the S trimer and keeps a high degree of conservation during SARS-CoV-2 evolution, making 553-49 a promising therapeutic reagent against the emerging Omicron and future variants of SARS-CoV-2.

Organizational Affiliation

Shanghai Fifth People's Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China.

Macromolecule Content

Total Structure Weight: 579.27 kDa
Atom Count: 35,604
Modeled Residue Count: 4,548
Deposited Residue Count: 5,193
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1,288	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1 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 A Focus chain B Focus chain C	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
mAb15 VH	D, F, H	225	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
mAb15 VL	E, G, I	218	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

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 ZA [auth C] SDF format, chain Z [auth B] SDF format, chain YA [auth C] SDF format, chain Y [auth B] SDF format, chain XA [auth C] SDF format, chain X [auth A] SDF format, chain WA [auth C] SDF format, chain W [auth A] SDF format, chain VA [auth C] SDF format, chain V [auth A] SDF format, chain UA [auth C] SDF format, chain U [auth A] SDF format, chain TA [auth C] SDF format, chain T [auth A] SDF format, chain SA [auth C] SDF format, chain S [auth A] SDF format, chain RA [auth C] SDF format, chain R [auth A] SDF format, chain QA [auth C] SDF format, chain Q [auth A] SDF format, chain PA [auth C] SDF format, chain P [auth A] SDF format, chain OA [auth C] SDF format, chain O [auth A] SDF format, chain NA [auth C] SDF format, chain N [auth A] SDF format, chain MA [auth B] SDF format, chain M [auth A] SDF format, chain LA [auth B] SDF format, chain L [auth A] SDF format, chain KA [auth B] SDF format, chain K [auth A] SDF format, chain JA [auth B] SDF format, chain J [auth A] SDF format, chain IA [auth B] SDF format, chain HA [auth B] SDF format, chain GA [auth B] SDF format, chain FA [auth B] SDF format, chain EA [auth B] SDF format, chain DA [auth B] SDF format, chain CA [auth B] SDF format, chain BB [auth C] SDF format, chain BA [auth B] SDF format, chain AB [auth C] SDF format, chain AA [auth B] MOL2 format, chain ZA [auth C] MOL2 format, chain Z [auth B] MOL2 format, chain YA [auth C] MOL2 format, chain Y [auth B] MOL2 format, chain XA [auth C] MOL2 format, chain X [auth A] MOL2 format, chain WA [auth C] MOL2 format, chain W [auth A] MOL2 format, chain VA [auth C] MOL2 format, chain V [auth A] MOL2 format, chain UA [auth C] MOL2 format, chain U [auth A] MOL2 format, chain TA [auth C] MOL2 format, chain T [auth A] MOL2 format, chain SA [auth C] MOL2 format, chain S [auth A] MOL2 format, chain RA [auth C] MOL2 format, chain R [auth A] MOL2 format, chain QA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain PA [auth C] MOL2 format, chain P [auth A] MOL2 format, chain OA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain BB [auth C] MOL2 format, chain BA [auth B] MOL2 format, chain AB [auth C] MOL2 format, chain AA [auth B] mmCIF format, chain ZA [auth C] mmCIF format, chain Z [auth B] mmCIF format, chain YA [auth C] mmCIF format, chain Y [auth B] mmCIF format, chain XA [auth C] mmCIF format, chain X [auth A] mmCIF format, chain WA [auth C] mmCIF format, chain W [auth A] mmCIF format, chain VA [auth C] mmCIF format, chain V [auth A] mmCIF format, chain UA [auth C] mmCIF format, chain U [auth A] mmCIF format, chain TA [auth C] mmCIF format, chain T [auth A] mmCIF format, chain SA [auth C] mmCIF format, chain S [auth A] mmCIF format, chain RA [auth C] mmCIF format, chain R [auth A] mmCIF format, chain QA [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain PA [auth C] mmCIF format, chain P [auth A] mmCIF format, chain OA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain NA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain BB [auth C] mmCIF format, chain BA [auth B] mmCIF format, chain AB [auth C] mmCIF format, chain AA [auth B]	AA [auth B] AB [auth C] BA [auth B] BB [auth C] CA [auth B] AA [auth B], AB [auth C], BA [auth B], BB [auth C], CA [auth B], DA [auth B], EA [auth B], FA [auth B], GA [auth B], HA [auth B], IA [auth B], J [auth A], JA [auth B], K [auth A], KA [auth B], L [auth A], LA [auth B], M [auth A], MA [auth B], N [auth A], NA [auth C], O [auth A], OA [auth C], P [auth A], PA [auth C], Q [auth A], QA [auth C], R [auth A], RA [auth C], S [auth A], SA [auth C], T [auth A], TA [auth C], U [auth A], UA [auth C], V [auth A], VA [auth C], W [auth A], WA [auth C], X [auth A], XA [auth C], Y [auth B], YA [auth C], Z [auth B], ZA [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth B] Focus chain AB [auth C] Focus chain BA [auth B] Focus chain BB [auth C] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain KA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain PA [auth C] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain R [auth A] Focus chain RA [auth C] Focus chain S [auth A] Focus chain SA [auth C] Focus chain T [auth A] Focus chain TA [auth C] Focus chain U [auth A] Focus chain UA [auth C] Focus chain V [auth A] Focus chain VA [auth C] Focus chain W [auth A] Focus chain WA [auth C] Focus chain X [auth A] Focus chain XA [auth C] Focus chain Y [auth B] Focus chain YA [auth C] Focus chain Z [auth B] Focus chain ZA [auth C] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth C] Focus chain BA [auth B] Focus chain BB [auth C] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain KA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain PA [auth C] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain R [auth A] Focus chain RA [auth C] Focus chain S [auth A] Focus chain SA [auth C] Focus chain T [auth A] Focus chain TA [auth C] Focus chain U [auth A] Focus chain UA [auth C] Focus chain V [auth A] Focus chain VA [auth C] Focus chain W [auth A] Focus chain WA [auth C] Focus chain X [auth A] Focus chain XA [auth C] Focus chain Y [auth B] Focus chain YA [auth C] Focus chain Z [auth B] Focus chain ZA [auth C]