8H01 | pdb_00008h01

SARS-CoV-2 Omicron BA.1 Spike glycoprotein in complex with rabbit monoclonal antibody 1H1 Fab in class 2 conformation

PDB DOI: https://doi.org/10.2210/pdb8H01/pdb
EM Map EMD-34408: EMDB EMDataResource

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

Deposited: 2022-09-27 Released: 2023-04-12
Deposition Author(s): Guo, H., Gao, Y., Lu, Y., Yang, H., Ji, X.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.70 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

Mechanism of a rabbit monoclonal antibody broadly neutralizing SARS-CoV-2 variants.

Guo, H., Yang, Y., Zhao, T., Lu, Y., Gao, Y., Li, T., Xiao, H., Chu, X., Zheng, L., Li, W., Cheng, H., Huang, H., Liu, Y., Lou, Y., Nguyen, H.C., Wu, C., Chen, Y., Yang, H., Ji, X.

(2023) Commun Biol 6: 364-364

PubMed: 37012333 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s42003-023-04759-5
Primary Citation Related Structures:
8GZZ, 8H00, 8H01, 8ITU

PubMed Abstract:
Due to the continuous evolution of SARS-CoV-2, the Omicron variant has emerged and exhibits severe immune evasion. The high number of mutations at key antigenic sites on the spike protein has made a large number of existing antibodies and vaccines ineffective against this variant. Therefore, it is urgent to develop efficient broad-spectrum neutralizing therapeutic drugs. Here we characterize a rabbit monoclonal antibody (RmAb) 1H1 with broad-spectrum neutralizing potency against Omicron sublineages including BA.1, BA.1.1, BA.2, BA.2.12.1, BA.2.75, BA.3 and BA.4/5. Cryo-electron microscopy (cryo-EM) structure determination of the BA.1 spike-1H1 Fab complexes shows that 1H1 targets a highly conserved region of RBD and avoids most of the circulating Omicron mutations, explaining its broad-spectrum neutralization potency. Our findings indicate 1H1 as a promising RmAb model for designing broad-spectrum neutralizing antibodies and shed light on the development of therapeutic agents as well as effective vaccines against newly emerging variants in the future.

Organizational Affiliation

The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, 210023, China.

Macromolecule Content

Total Structure Weight: 511.13 kDa
Atom Count: 30,144
Modeled Residue Count: 3,803
Deposited Residue Count: 4,557
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, C	1,286	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 39 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: 9	Glycosylation Focus chain A Focus chain B Focus chain C	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
rabbit monoclonal antibody 1H1 Fab light chain	D, F, H	111	Oryctolagus cuniculus	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
rabbit monoclonal antibody 1H1 Fab heavy chain	E, G, I	122	Oryctolagus cuniculus	Mutation(s): 0

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	J [auth O], K [auth J], L [auth K], M [auth L], N [auth M], J [auth O], K [auth J], L [auth K], M [auth L], N [auth M], O [auth N], P, Q, R, S, T, U, V, W, X	2		N-Glycosylation	Interactions Focus chain J [auth O] Focus chain K [auth J] Focus chain L [auth K] Focus chain M [auth L] Focus chain N [auth M] Focus chain O [auth N] Focus chain P Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V Focus chain W Focus chain X Interactions & Density Focus chain J [auth O] Focus chain K [auth J] Focus chain L [auth K] Focus chain M [auth L] Focus chain N [auth M] Focus chain O [auth N] Focus chain P Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V Focus chain W Focus chain X
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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 Z [auth A] SDF format, chain Y [auth A] SDF format, chain LA [auth C] SDF format, chain KA [auth C] SDF format, chain JA [auth C] SDF format, chain IA [auth C] SDF format, chain HA [auth C] SDF format, chain GA [auth B] SDF format, chain FA [auth B] SDF format, chain EA [auth B] SDF format, chain DA [auth B] SDF format, chain CA [auth A] SDF format, chain BA [auth A] SDF format, chain AA [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain KA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain GA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain CA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain AA [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain KA [auth C] mmCIF format, chain JA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain GA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain CA [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain AA [auth A]	AA [auth A] BA [auth A] CA [auth A] DA [auth B] EA [auth B] AA [auth A], BA [auth A], CA [auth A], DA [auth B], EA [auth B], FA [auth B], GA [auth B], HA [auth C], IA [auth C], JA [auth C], KA [auth C], LA [auth C], Y [auth A], Z [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain Y [auth A] Focus chain Z [auth A]