9BJ3 | pdb_00009bj3

Structure of the SARS-CoV-2 S 6P trimer complex with the human neutralizing antibody Fab fragment, C1596

PDB DOI: https://doi.org/10.2210/pdb9BJ3/pdb
EM Map EMD-44628: EMDB EMDataResource

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

Deposited: 2024-04-24 Released: 2025-03-05
Deposition Author(s): Rubio, A.A., Abernathy, M.E., Barnes, C.O.
Funding Organization(s): Howard Hughes Medical Institute (HHMI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.04 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Bispecific antibodies targeting the N-terminal and receptor binding domains potently neutralize SARS-CoV-2 variants of concern.

Rubio, A.A., Baharani, V.A., Dadonaite, B., Parada, M., Abernathy, M.E., Wang, Z., Lee, Y.E., Eso, M.R., Phung, J., Ramos, I., Chen, T., El Nesr, G., Bloom, J.D., Bieniasz, P.D., Nussenzweig, M.C., Barnes, C.O.

(2025) Sci Transl Med 17: eadq5720-eadq5720

PubMed: 40043139 Search on PubMed
DOI: https://doi.org/10.1126/scitranslmed.adq5720
Primary Citation Related Structures:
9BJ2, 9BJ3, 9BJ4

PubMed Abstract:
The ongoing emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) that reduce the effectiveness of antibody therapeutics necessitates development of next-generation antibody modalities that are resilient to viral evolution. Here, we characterized amino-terminal domain (NTD)- and receptor binding domain (RBD)-specific monoclonal antibodies previously isolated from coronavirus disease 2019 (COVID-19) convalescent donors for their activity against emergent SARS-CoV-2 VOCs. Among these, the NTD-specific antibody C1596 displayed the greatest breadth of binding to VOCs, with cryo-electron microscopy structural analysis revealing recognition of a distinct NTD epitope outside of the site i antigenic supersite. Given C1596's favorable binding profile, we designed a series of bispecific antibodies (bsAbs), termed CoV2-biRNs, that featured both NTD and RBD specificities. Two of the C1596-inclusive bsAbs, CoV2-biRN5 and CoV2-biRN7, retained potent in vitro neutralization activity against all Omicron variants tested, including XBB.1.5, BA.2.86, and JN.1, contrasting the diminished potency of parental antibodies delivered as monotherapies or as a cocktail. Furthermore, prophylactic delivery of CoV2-biRN5 reduced the viral load within the lungs of K18-hACE2 mice after challenge with SARS-CoV-2 XBB.1.5. In conclusion, NTD-RBD bsAbs offer promising potential for the design of resilient, next-generation antibody therapeutics against SARS-CoV-2 VOCs.

Organizational Affiliation

Stanford Biosciences, Stanford School of Medicine, Stanford, CA 94305, USA.

Macromolecule Content

Total Structure Weight: 588.88 kDa
Atom Count: 30,621
Modeled Residue Count: 3,819
Deposited Residue Count: 5,178
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, I [auth S]	1,271	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 6 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 A Focus chain B Focus chain I [auth S]	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
C1596 Fab Heavy Chain	C, E, G [auth H]	240	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

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
C1596 Light Chain	D, F, H [auth L]	215	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

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	BA [auth b], CA [auth c], DA [auth d], FA [auth f], GA [auth g], BA [auth b], CA [auth c], DA [auth d], FA [auth f], GA [auth g], HA [auth h], IA [auth i], J [auth G], L [auth J], LA [auth l], M [auth K], MA [auth m], N [auth M], O [auth N], R [auth Q], S [auth R], T, V, W, X, Y	2		N-Glycosylation	Interactions Focus chain BA [auth b] Focus chain CA [auth c] Focus chain DA [auth d] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain IA [auth i] Focus chain J [auth G] Focus chain L [auth J] Focus chain LA [auth l] Focus chain M [auth K] Focus chain MA [auth m] Focus chain N [auth M] Focus chain O [auth N] Focus chain R [auth Q] Focus chain S [auth R] Focus chain T Focus chain V Focus chain W Focus chain X Focus chain Y Interactions & Density Focus chain BA [auth b] Focus chain CA [auth c] Focus chain DA [auth d] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain IA [auth i] Focus chain J [auth G] Focus chain L [auth J] Focus chain LA [auth l] Focus chain M [auth K] Focus chain MA [auth m] Focus chain N [auth M] Focus chain O [auth N] Focus chain R [auth Q] Focus chain S [auth R] Focus chain T Focus chain V Focus chain W Focus chain X Focus chain Y
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	EA [auth e], K [auth I], U	4		N-Glycosylation	Interactions Focus chain EA [auth e] Focus chain K [auth I] Focus chain U Interactions & Density Focus chain EA [auth e] Focus chain K [auth I] Focus chain U
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a], JA [auth j], KA [auth k], P [auth O], Q [auth P], AA [auth a], JA [auth j], KA [auth k], P [auth O], Q [auth P], Z	3		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain JA [auth j] Focus chain KA [auth k] Focus chain P [auth O] Focus chain Q [auth P] Focus chain Z Interactions & Density Focus chain AA [auth a] Focus chain JA [auth j] Focus chain KA [auth k] Focus chain P [auth O] Focus chain Q [auth P] Focus chain Z
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

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 S] SDF format, chain BB [auth S] SDF format, chain CB [auth S] SDF format, chain DB [auth S] SDF format, chain EB [auth S] SDF format, chain NA [auth A] SDF format, chain OA [auth A] SDF format, chain PA [auth A] SDF format, chain QA [auth A] SDF format, chain RA [auth A] SDF format, chain SA [auth A] SDF format, chain TA [auth B] SDF format, chain UA [auth B] SDF format, chain VA [auth B] SDF format, chain WA [auth B] SDF format, chain XA [auth B] SDF format, chain YA [auth B] SDF format, chain ZA [auth S] MOL2 format, chain AB [auth S] MOL2 format, chain BB [auth S] MOL2 format, chain CB [auth S] MOL2 format, chain DB [auth S] MOL2 format, chain EB [auth S] MOL2 format, chain NA [auth A] MOL2 format, chain OA [auth A] MOL2 format, chain PA [auth A] MOL2 format, chain QA [auth A] MOL2 format, chain RA [auth A] MOL2 format, chain SA [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain UA [auth B] MOL2 format, chain VA [auth B] MOL2 format, chain WA [auth B] MOL2 format, chain XA [auth B] MOL2 format, chain YA [auth B] MOL2 format, chain ZA [auth S] mmCIF format, chain AB [auth S] mmCIF format, chain BB [auth S] mmCIF format, chain CB [auth S] mmCIF format, chain DB [auth S] mmCIF format, chain EB [auth S] mmCIF format, chain NA [auth A] mmCIF format, chain OA [auth A] mmCIF format, chain PA [auth A] mmCIF format, chain QA [auth A] mmCIF format, chain RA [auth A] mmCIF format, chain SA [auth A] mmCIF format, chain TA [auth B] mmCIF format, chain UA [auth B] mmCIF format, chain VA [auth B] mmCIF format, chain WA [auth B] mmCIF format, chain XA [auth B] mmCIF format, chain YA [auth B] mmCIF format, chain ZA [auth S]	AB [auth S] BB [auth S] CB [auth S] DB [auth S] EB [auth S] AB [auth S], BB [auth S], CB [auth S], DB [auth S], EB [auth S], NA [auth A], OA [auth A], PA [auth A], QA [auth A], RA [auth A], SA [auth A], TA [auth B], UA [auth B], VA [auth B], WA [auth B], XA [auth B], YA [auth B], ZA [auth S]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth S] Focus chain BB [auth S] Focus chain CB [auth S] Focus chain DB [auth S] Focus chain EB [auth S] Focus chain NA [auth A] Focus chain OA [auth A] Focus chain PA [auth A] Focus chain QA [auth A] Focus chain RA [auth A] Focus chain SA [auth A] Focus chain TA [auth B] Focus chain UA [auth B] Focus chain VA [auth B] Focus chain WA [auth B] Focus chain XA [auth B] Focus chain YA [auth B] Focus chain ZA [auth S] Interactions & Density Focus chain AB [auth S] Focus chain BB [auth S] Focus chain CB [auth S] Focus chain DB [auth S] Focus chain EB [auth S] Focus chain NA [auth A] Focus chain OA [auth A] Focus chain PA [auth A] Focus chain QA [auth A] Focus chain RA [auth A] Focus chain SA [auth A] Focus chain TA [auth B] Focus chain UA [auth B] Focus chain VA [auth B] Focus chain WA [auth B] Focus chain XA [auth B] Focus chain YA [auth B] Focus chain ZA [auth S]