7UKL | pdb_00007ukl

Cryo-EM structure of Antibody 12-16 in complex with prefusion SARS-CoV-2 Spike glycoprotein

PDB DOI: https://doi.org/10.2210/pdb7UKL/pdb
EM Map EMD-26583: EMDB EMDataResource

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

Deposited: 2022-04-01 Released: 2023-10-04
Deposition Author(s): Casner, R.G., Shapiro, L.
Funding Organization(s): Jack Ma Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.09 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Antibodies targeting a quaternary site on SARS-CoV-2 spike glycoprotein prevent viral receptor engagement by conformational locking.

Liu, L., Casner, R.G., Guo, Y., Wang, Q., Iketani, S., Chan, J.F., Yu, J., Dadonaite, B., Nair, M.S., Mohri, H., Reddem, E.R., Yuan, S., Poon, V.K., Chan, C.C., Yuen, K.Y., Sheng, Z., Huang, Y., Bloom, J.D., Shapiro, L., Ho, D.D.

(2023) Immunity 56: 2442

PubMed: 37776849 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.immuni.2023.09.003
Primary Citation Related Structures:
7UKL, 7UKM

PubMed Abstract:
SARS-CoV-2 continues to evolve, with many variants evading clinically authorized antibodies. To isolate monoclonal antibodies (mAbs) with broadly neutralizing capacities against the virus, we screened serum samples from convalescing COVID-19 patients. We isolated two mAbs, 12-16 and 12-19, which neutralized all SARS-CoV-2 variants tested, including the XBB subvariants, and prevented infection in hamsters challenged with Omicron BA.1 intranasally. Structurally, both antibodies targeted a conserved quaternary epitope located at the interface between the N-terminal domain and subdomain 1, uncovering a site of vulnerability on SARS-CoV-2 spike. These antibodies prevented viral receptor engagement by locking the receptor-binding domain (RBD) of spike in the down conformation, revealing a mechanism of virus neutralization for non-RBD antibodies. Deep mutational scanning showed that SARS-CoV-2 could mutate to escape 12-19, but such mutations are rarely found in circulating viruses. Antibodies 12-16 and 12-19 hold promise as prophylactic agents for immunocompromised persons who do not respond robustly to COVID-19 vaccines.

Organizational Affiliation

Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA. Electronic address: ll3411@cumc.columbia.edu.

Macromolecule Content

Total Structure Weight: 513.06 kDa
Atom Count: 30,234
Modeled Residue Count: 3,795
Deposited Residue Count: 4,539
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
12-16 Fab Light Chain	A [auth Y], D [auth L], I [auth N]	108	Homo sapiens	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	B, E [auth C], F [auth A]	1,273	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: 16	Glycosylation Focus chain B Focus chain E [auth C] Focus chain F [auth A]	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
12-16 Fab Heavy Chain	C [auth X], G [auth H], H [auth M]	132	Homo sapiens	Mutation(s): 0

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