8HRD | pdb_00008hrd

Crystal structure of the receptor binding domain of SARS-CoV-2 Delta variant in complex with IMCAS74 Fab and W14 Fab

PDB DOI: https://doi.org/10.2210/pdb8HRD/pdb

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

Deposited: 2022-12-15 Released: 2023-12-20
Deposition Author(s): Zhao, R.C., Wu, L.L., Han, P.
Funding Organization(s): Chinese Academy of Sciences

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.86 Å
R-Value Free:
0.244 (Depositor), 0.245 (DCC)
R-Value Work:
0.212 (Depositor), 0.213 (DCC)
R-Value Observed:
0.213 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Defining a de novo non-RBM antibody as RBD-8 and its synergistic rescue of immune-evaded antibodies to neutralize Omicron SARS-CoV-2.

Rao, X., Zhao, R., Tong, Z., Guo, S., Peng, W., Liu, K., Li, S., Wu, L., Tong, J., Chai, Y., Han, P., Wang, F., Jia, P., Li, Z., Zhao, X., Li, D., Zhang, R., Zhang, X., Zou, W., Li, W., Wang, Q., Gao, G.F., Wu, Y., Dai, L., Gao, F.

(2023) Proc Natl Acad Sci U S A 120: e2314193120-e2314193120

PubMed: 38109549 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.2314193120
Primary Citation Related Structures:
7Y3N, 7Y3O, 8HRD

PubMed Abstract:
Currently, monoclonal antibodies (MAbs) targeting the SARS-CoV-2 receptor binding domain (RBD) of spike (S) protein are classified into seven classes based on their binding epitopes. However, most of these antibodies are seriously impaired by SARS-CoV-2 Omicron and its subvariants, especially the recent BQ.1.1, XBB and its derivatives. Identification of broadly neutralizing MAbs against currently circulating variants is imperative. In this study, we identified a "breathing" cryptic epitope in the S protein, named as RBD-8. Two human MAbs, BIOLS56 and IMCAS74, were isolated recognizing this epitope with broad neutralization abilities against tested sarbecoviruses, including SARS-CoV, pangolin-origin coronaviruses, and all the SARS-CoV-2 variants tested (Omicron BA.4/BA.5, BQ.1.1, and XBB subvariants). Searching through the literature, some more RBD-8 MAbs were defined. More importantly, BIOLS56 rescues the immune-evaded antibody, RBD-5 MAb IMCAS-L4.65, by making a bispecific MAb, to neutralize BQ.1 and BQ.1.1, thereby producing an MAb to cover all the currently circulating Omicron subvariants. Structural analysis reveals that the neutralization effect of RBD-8 antibodies depends on the extent of epitope exposure, which is affected by the angle of antibody binding and the number of up-RBDs induced by angiotensin-converting enzyme 2 binding. This cryptic epitope which recognizes non- receptor binding motif (non-RBM) provides guidance for the development of universal therapeutic antibodies and vaccines against COVID-19.

Organizational Affiliation

Laboratory of Protein Engineering and Vaccines, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.

Macromolecule Content

Total Structure Weight: 487.97 kDa
Atom Count: 33,039
Modeled Residue Count: 4,316
Deposited Residue Count: 4,496
Unique protein chains: 5

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A, F [auth B], K, P [auth T]	223	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 2 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 F [auth B] Focus chain K Focus chain P [auth T]	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
IMCAS74 Fab heavy chain	B [auth O], G [auth C], L, Q [auth W]	235	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
IMCAS74 Fab light chain	C [auth P], H [auth E], M, R [auth X]	217	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
W14 Fab heavy chain	D, I [auth G], N, S [auth Y]	234	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
W14 Fab light chain	E [auth F], J [auth H], O [auth Q], T [auth Z]	215	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download:Ideal Coordinates CCD File SDF format, chain U [auth A] SDF format, chain V [auth B] SDF format, chain W [auth K] SDF format, chain X [auth T] MOL2 format, chain U [auth A] MOL2 format, chain V [auth B] MOL2 format, chain W [auth K] MOL2 format, chain X [auth T] mmCIF format, chain U [auth A] mmCIF format, chain V [auth B] mmCIF format, chain W [auth K] mmCIF format, chain X [auth T]	U [auth A], V [auth B], W [auth K], X [auth T]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain U [auth A] Focus chain V [auth B] Focus chain W [auth K] Focus chain X [auth T] Interactions & Density Focus chain U [auth A] Focus chain V [auth B] Focus chain W [auth K] Focus chain X [auth T]