7WQV | pdb_00007wqv

Crystal structure of a neutralizing monoclonal antibody (Ab08) in complex with SARS-CoV-2 receptor-binding domain (RBD)

PDB DOI: https://doi.org/10.2210/pdb7WQV/pdb

Classification: VIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
Expression System: Trichoplusia ni, Escherichia coli MC1061
Mutation(s): No

Deposited: 2022-01-26 Released: 2023-01-25
Deposition Author(s): Zha, J., Meng, L., Zhang, X., Li, D.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.251 (Depositor), 0.241 (DCC)
R-Value Work:
0.220 (Depositor), 0.218 (DCC)
R-Value Observed:
0.221 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

A Spike-destructing human antibody effectively neutralizes Omicron-included SARS-CoV-2 variants with therapeutic efficacy.

Meng, L., Zha, J., Zhou, B., Cao, L., Jiang, C., Zhu, Y., Li, T., Lu, L., Zhang, J., Yang, H., Feng, J., Gu, Z., Tang, H., Jiang, L., Li, D., Lavillette, D., Zhang, X.

(2023) PLoS Pathog 19: e1011085-e1011085

PubMed: 36706160 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1371/journal.ppat.1011085
Primary Citation Related Structures:
7WQV

PubMed Abstract:
Neutralizing antibodies (nAbs) are important assets to fight COVID-19, but most existing nAbs lose the activities against Omicron subvariants. Here, we report a human monoclonal antibody (Ab08) isolated from a convalescent patient infected with the prototype strain (Wuhan-Hu-1). Ab08 binds to the receptor-binding domain (RBD) with pico-molar affinity (230 pM), effectively neutralizes SARS-CoV-2 and variants of concern (VOCs) including Alpha, Beta, Gamma, Mu, Omicron BA.1 and BA.2, and to a lesser extent for Delta and Omicron BA.4/BA.5 which bear the L452R mutation. Of medical importance, Ab08 shows therapeutic efficacy in SARS-CoV-2-infected hACE2 mice. X-ray crystallography of the Ab08-RBD complex reveals an antibody footprint largely in the β-strand core and away from the ACE2-binding motif. Negative staining electron-microscopy suggests a neutralizing mechanism through which Ab08 destructs the Spike trimer. Together, our work identifies a nAb with therapeutic potential for COVID-19.

Organizational Affiliation

Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences/University of Chinese Academy of Sciences, Shanghai, China.

Macromolecule Content

Total Structure Weight: 463.81 kDa
Atom Count: 26,586
Modeled Residue Count: 3,466
Deposited Residue Count: 4,296
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A, C, E, G, I A, C, E, G, I, K, M, O	234	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: 1	Glycosylation Focus chain A Focus chain C Focus chain E Focus chain G Focus chain O	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ab08	B, D, F, H, J B, D, F, H, J, L, N, P	303	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: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	Q, S	2		N-Glycosylation	Interactions Focus chain Q Focus chain S Interactions & Density Focus chain Q Focus chain S
Glycosylation Resources
GlyTouCan: G86851RC GlyCosmos: G86851RC GlyGen: G86851RC

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose	R	2		N-Glycosylation	Interactions Focus chain R Interactions & Density Focus chain R
Glycosylation Resources
GlyTouCan: G80587NA GlyCosmos: G80587NA GlyGen: G80587NA

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain Y [auth C] SDF format, chain KA [auth O] MOL2 format, chain Y [auth C] MOL2 format, chain KA [auth O] mmCIF format, chain Y [auth C] mmCIF format, chain KA [auth O]	KA [auth O], Y [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain KA [auth O] Focus chain Y [auth C] Interactions & Density Focus chain KA [auth O] Focus chain Y [auth C]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain DA [auth H] SDF format, chain GA [auth J] SDF format, chain HA [auth J] SDF format, chain LA [auth O] SDF format, chain T [auth A] SDF format, chain V [auth B] SDF format, chain Z [auth D] SDF format, chain U [auth A] SDF format, chain MA [auth P] SDF format, chain FA [auth I] SDF format, chain EA [auth I] MOL2 format, chain DA [auth H] MOL2 format, chain GA [auth J] MOL2 format, chain HA [auth J] MOL2 format, chain LA [auth O] MOL2 format, chain T [auth A] MOL2 format, chain V [auth B] MOL2 format, chain Z [auth D] MOL2 format, chain U [auth A] MOL2 format, chain MA [auth P] MOL2 format, chain FA [auth I] MOL2 format, chain EA [auth I] mmCIF format, chain DA [auth H] mmCIF format, chain GA [auth J] mmCIF format, chain HA [auth J] mmCIF format, chain LA [auth O] mmCIF format, chain T [auth A] mmCIF format, chain V [auth B] mmCIF format, chain Z [auth D] mmCIF format, chain U [auth A] mmCIF format, chain MA [auth P] mmCIF format, chain FA [auth I] mmCIF format, chain EA [auth I]	DA [auth H] EA [auth I] FA [auth I] GA [auth J] HA [auth J] DA [auth H], EA [auth I], FA [auth I], GA [auth J], HA [auth J], LA [auth O], MA [auth P], T [auth A], U [auth A], V [auth B], Z [auth D]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain DA [auth H] Focus chain EA [auth I] Focus chain FA [auth I] Focus chain GA [auth J] Focus chain HA [auth J] Focus chain LA [auth O] Focus chain MA [auth P] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth B] Focus chain Z [auth D] Interactions & Density Focus chain DA [auth H] Focus chain EA [auth I] Focus chain FA [auth I] Focus chain GA [auth J] Focus chain HA [auth J] Focus chain LA [auth O] Focus chain MA [auth P] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth B] Focus chain Z [auth D]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain BA [auth F] SDF format, chain JA [auth N] SDF format, chain W [auth B] SDF format, chain NA [auth P] SDF format, chain IA [auth L] SDF format, chain AA [auth D] MOL2 format, chain BA [auth F] MOL2 format, chain JA [auth N] MOL2 format, chain W [auth B] MOL2 format, chain NA [auth P] MOL2 format, chain IA [auth L] MOL2 format, chain AA [auth D] mmCIF format, chain BA [auth F] mmCIF format, chain JA [auth N] mmCIF format, chain W [auth B] mmCIF format, chain NA [auth P] mmCIF format, chain IA [auth L] mmCIF format, chain AA [auth D]	AA [auth D] BA [auth F] IA [auth L] JA [auth N] NA [auth P] AA [auth D], BA [auth F], IA [auth L], JA [auth N], NA [auth P], W [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth F] Focus chain IA [auth L] Focus chain JA [auth N] Focus chain NA [auth P] Focus chain W [auth B] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth F] Focus chain IA [auth L] Focus chain JA [auth N] Focus chain NA [auth P] Focus chain W [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain CA [auth G] SDF format, chain X [auth B] MOL2 format, chain CA [auth G] MOL2 format, chain X [auth B] mmCIF format, chain CA [auth G] mmCIF format, chain X [auth B]	CA [auth G], X [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain CA [auth G] Focus chain X [auth B] Interactions & Density Focus chain CA [auth G] Focus chain X [auth B]