7WS9

Structures of Omicron Spike complexes illuminate broad-spectrum neutralizing antibody development

PDB DOI: https://doi.org/10.2210/pdb7WS9/pdb
EM Map EMD-32751: EMDB EMDataResource

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

Deposited: 2022-01-28 Released: 2022-06-01
Deposition Author(s): Guo, H., Gao, Y., Ji, X., Yang, H.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.90 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.

Macromolecule Content

Total Structure Weight: 479.38 kDa
Atom Count: 29,710
Modelled Residue Count: 3,691
Deposited Residue Count: 4,210
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1,205	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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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Processed angiotensin-converting enzyme 2	D	595	Homo sapiens	Mutation(s): 0 Gene Names: ACE2, UNQ868/PRO1885
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYF1 (Homo sapiens) Explore Q9BYF1 Go to UniProtKB: Q9BYF1
PHAROS: Q9BYF1 GTEx: ENSG00000130234
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9BYF1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth O], F [auth E], G [auth F], H [auth G], I [auth H], E [auth O], F [auth E], G [auth F], H [auth G], I [auth H], J [auth I], K [auth J], L [auth K], M [auth L], N [auth M], O [auth N], P, Q, R	2		N-Glycosylation	Interactions Focus chain E [auth O] Focus chain F [auth E] Focus chain G [auth F] Focus chain H [auth G] Focus chain I [auth H] Focus chain J [auth I] 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 Interactions & Density Focus chain E [auth O] Focus chain F [auth E] Focus chain G [auth F] Focus chain H [auth G] Focus chain I [auth H] Focus chain J [auth I] 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
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 D] SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth C] SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D]	AA [auth D] BA [auth D] CA [auth D] DA [auth D] S [auth A] AA [auth D], BA [auth D], CA [auth D], DA [auth D], S [auth A], T [auth A], U [auth A], V [auth B], W [auth B], X [auth C], Y [auth D], Z [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth C] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth C] Focus chain Y [auth D] Focus chain Z [auth D]