9LYO | pdb_00009lyo

Alpha SARS-CoV-2 spike protein in complex with REGN10987 Fab homologue.

PDB DOI: https://doi.org/10.2210/pdb9LYO/pdb
EM Map EMD-63513: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2025-02-20 Released: 2025-04-02
Deposition Author(s): Kocharovskaya, M.V., Pichkur, E.B., Shenkarev, Z.O., Lyukmanova, E.N.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.07 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structure and dynamics of Alpha B.1.1.7 SARS-CoV-2 S-protein in complex with Fab of neutralizing antibody REGN10987.

Kocharovskaya, M.V., Pichkur, E.B., Ivannikov, A.D., Kharlampieva, D.D., Grafskaia, E.N., Lyukmanova, E.N., Kirpichnikov, M.P., Shenkarev, Z.O.

(2025) Biochem Biophys Res Commun 755: 151558-151558

PubMed: 40043614 Search on PubMed
DOI: https://doi.org/10.1016/j.bbrc.2025.151558
Primary Citation Related Structures:
9LYO, 9LYP

PubMed Abstract:
One of the approaches for treatment of COVID-19 is a use of neutralizing antibodies (nAbs). The study of the mechanisms by which nAbs recognize different strains of SARS-CoV-2 may facilitate the development of new drugs and vaccines against the coronavirus infection. In this work, we present the 3.1 Å resolution cryo-electron microscopy structure of a full-length trimeric spike-protein (S-protein) of the SARS-CoV-2 Alpha (B.1.1.7) variant in complex with the Fab of the REGN10987 nAb. In the complex, two receptor-binding domains (RBDs) of the S-protein were observed in the 'up' state, whereas third RBD was in the 'down' state. This distinguishes the obtained structure from the complex of Delta (B.1.617.2) S-protein with REGN10987-Fab, where only one RBD was in the 'up' state. Probably some of the substituted residues (K478T, A570D, and S982A) located at the interprotomer interfaces are responsible for the greater Alpha S-protein opening upon the REGN10987-Fab binding. The Fab identically binds to the RBD in the both 'up' and 'down' conformations. The RBD-Fab interaction interface was refined to a resolution of 3.6 Å. The antibody binds to the receptor-binding motif (RBM), which prevents the S-protein from the binding to its receptor, angiotensin-converting enzyme 2 (ACE-2). Comparison with the structures of the Wuhan (wild type) and Delta RBD variants in complex with REGN10987-Fab revealed that the N501Y and T478K/L452R mutations presented in the RBM of the Alpha and Delta variants, respectively, do not affect the mode of the RBD-Fab interaction.

Organizational Affiliation

Department of Structural Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997, Moscow, Russia; Moscow Center for Advanced Studies, 123592, Moscow, Russia.

Macromolecule Content

Total Structure Weight: 586.07 kDa
Atom Count: 34,834
Modeled Residue Count: 4,371
Deposited Residue Count: 5,181
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
REGN10987 Fab homologue (Light chain)	A [auth i], F [auth g], H [auth l]	218	Homo sapiens	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
REGN10987 Fab homologue (Heavy chain)	B [auth j], G [auth h], I [auth n]	223	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	C [auth A], D [auth B], E [auth C]	1,286	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 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 C [auth A] Focus chain D [auth B] Focus chain E [auth C]	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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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	AA [auth U], BA [auth V], CA [auth W], DA [auth X], EA [auth Y], AA [auth U], BA [auth V], CA [auth W], DA [auth X], EA [auth Y], FA [auth Z], GA [auth a], HA [auth b], IA [auth c], J [auth P], JA [auth d], K [auth D], KA [auth e], L [auth E], LA [auth f], M [auth F], MA [auth k], N [auth G], NA [auth m], O [auth H], P [auth I], Q [auth J], R [auth K], S [auth L], T [auth M], U [auth N], V [auth O], W [auth Q], X [auth R], Y [auth S], Z [auth T]	2		N-Glycosylation	Interactions Focus chain AA [auth U] Focus chain BA [auth V] Focus chain CA [auth W] Focus chain DA [auth X] Focus chain EA [auth Y] Focus chain FA [auth Z] Focus chain GA [auth a] Focus chain HA [auth b] Focus chain IA [auth c] Focus chain J [auth P] Focus chain JA [auth d] Focus chain K [auth D] Focus chain KA [auth e] Focus chain L [auth E] Focus chain LA [auth f] Focus chain M [auth F] Focus chain MA [auth k] Focus chain N [auth G] Focus chain NA [auth m] Focus chain O [auth H] Focus chain P [auth I] Focus chain Q [auth J] Focus chain R [auth K] Focus chain S [auth L] Focus chain T [auth M] Focus chain U [auth N] Focus chain V [auth O] Focus chain W [auth Q] Focus chain X [auth R] Focus chain Y [auth S] Focus chain Z [auth T] Interactions & Density Focus chain AA [auth U] Focus chain BA [auth V] Focus chain CA [auth W] Focus chain DA [auth X] Focus chain EA [auth Y] Focus chain FA [auth Z] Focus chain GA [auth a] Focus chain HA [auth b] Focus chain IA [auth c] Focus chain J [auth P] Focus chain JA [auth d] Focus chain K [auth D] Focus chain KA [auth e] Focus chain L [auth E] Focus chain LA [auth f] Focus chain M [auth F] Focus chain MA [auth k] Focus chain N [auth G] Focus chain NA [auth m] Focus chain O [auth H] Focus chain P [auth I] Focus chain Q [auth J] Focus chain R [auth K] Focus chain S [auth L] Focus chain T [auth M] Focus chain U [auth N] Focus chain V [auth O] Focus chain W [auth Q] Focus chain X [auth R] Focus chain Y [auth S] Focus chain Z [auth T]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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