8H01

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 1.0 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

DOI: https://doi.org/10.1038/s42003-023-04759-5

Macromolecule Content

Total Structure Weight: 511.13 kDa
Atom Count: 30,144
Modelled Residue Count: 3,803
Deposited Residue Count: 4,557
Unique protein chains: 3

Macromolecules

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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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTC2
Sequence Annotations Expand
Reference Sequence

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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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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 AA [auth A] SDF format, chain BA [auth A] SDF format, chain CA [auth A] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain HA [auth C] SDF format, chain IA [auth C] SDF format, chain JA [auth C] SDF format, chain KA [auth C] SDF format, chain LA [auth C] SDF format, chain Y [auth A] SDF format, chain Z [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain KA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain Y [auth A] MOL2 format, chain Z [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]