8Y16

Cryo-EM structure of SARS-CoV-2 Omicron JN.1 spike protein in complex with human ACE2

PDB DOI: https://doi.org/10.2210/pdb8Y16/pdb
EM Map EMD-38826: EMDB EMDataResource

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

Deposited: 2024-01-23 Released: 2024-07-03
Deposition Author(s): Li, L.J., Gu, Y.H., Qi, J.X., Gao, G.F.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.98 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

Spike structures, receptor binding and immune escape of SARS-CoV-2 Omicron recently-circulating BA.2.86.1, JN.1, EG.5, EG.5.1 and HV.1 sub-variants

Li, L.J., Gao, G.F.

To be published.

Macromolecule Content

Total Structure Weight: 643.46 kDa
Atom Count: 39,510
Modelled Residue Count: 4,820
Deposited Residue Count: 5,553
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Angiotensin-converting enzyme 2	A, E, F	603	Homo sapiens	Mutation(s): 0 Gene Names: ACE2, UNQ868/PRO1885 EC: 3.4.17.23 (PDB Primary Data), 3.4.17 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYF1 (Homo sapiens) Explore Q9BYF1 Go to UniProtKB: Q9BYF1
GTEx: ENSG00000130234
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9BYF1
Glycosylation
Glycosylation Sites: 6	Glycosylation Focus chain A Focus chain E Focus chain F	Go to GlyGen: Q9BYF1-1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	B, C, D	1,248	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 66 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
Glycosylation
Glycosylation Sites: 11	Glycosylation Focus chain B Focus chain C Focus chain D	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, H, R, S, V G, H, R, S, V, W	3		N-Glycosylation	Interactions Focus chain G Focus chain H Focus chain R Focus chain S Focus chain V Focus chain W Interactions & Density Focus chain G Focus chain H Focus chain R Focus chain S Focus chain V Focus chain W
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

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	I, J, K, L, M I, J, K, L, M, N, O, P, Q, T, U, X, Y	2		N-Glycosylation	Interactions Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Focus chain N Focus chain O Focus chain P Focus chain Q Focus chain T Focus chain U Focus chain X Focus chain Y Interactions & Density Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Focus chain N Focus chain O Focus chain P Focus chain Q Focus chain T Focus chain U Focus chain X Focus chain Y
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 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 AB [auth D] SDF format, chain BA [auth A] SDF format, chain BB [auth D] SDF format, chain CA [auth B] SDF format, chain CB [auth D] SDF format, chain DA [auth B] SDF format, chain DB [auth D] SDF format, chain EA [auth B] SDF format, chain EB [auth D] SDF format, chain FA [auth B] SDF format, chain FB [auth D] SDF format, chain GA [auth B] SDF format, chain GB [auth D] SDF format, chain HA [auth B] SDF format, chain IA [auth B] SDF format, chain IB [auth E] SDF format, chain JA [auth B] SDF format, chain JB [auth E] SDF format, chain KA [auth C] SDF format, chain LA [auth C] SDF format, chain LB [auth F] SDF format, chain MA [auth C] SDF format, chain MB [auth F] SDF format, chain NA [auth C] SDF format, chain OA [auth C] SDF format, chain PA [auth C] SDF format, chain QA [auth C] SDF format, chain RA [auth C] SDF format, chain SA [auth C] SDF format, chain TA [auth D] SDF format, chain UA [auth D] SDF format, chain VA [auth D] SDF format, chain WA [auth D] SDF format, chain XA [auth D] SDF format, chain YA [auth D] SDF format, chain ZA [auth D] MOL2 format, chain AA [auth A] MOL2 format, chain AB [auth D] MOL2 format, chain BA [auth A] MOL2 format, chain BB [auth D] MOL2 format, chain CA [auth B] MOL2 format, chain CB [auth D] MOL2 format, chain DA [auth B] MOL2 format, chain DB [auth D] MOL2 format, chain EA [auth B] MOL2 format, chain EB [auth D] MOL2 format, chain FA [auth B] MOL2 format, chain FB [auth D] MOL2 format, chain GA [auth B] MOL2 format, chain GB [auth D] MOL2 format, chain HA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain IB [auth E] MOL2 format, chain JA [auth B] MOL2 format, chain JB [auth E] MOL2 format, chain KA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain LB [auth F] MOL2 format, chain MA [auth C] MOL2 format, chain MB [auth F] MOL2 format, chain NA [auth C] MOL2 format, chain OA [auth C] MOL2 format, chain PA [auth C] MOL2 format, chain QA [auth C] MOL2 format, chain RA [auth C] MOL2 format, chain SA [auth C] MOL2 format, chain TA [auth D] MOL2 format, chain UA [auth D] MOL2 format, chain VA [auth D] MOL2 format, chain WA [auth D] MOL2 format, chain XA [auth D] MOL2 format, chain YA [auth D] MOL2 format, chain ZA [auth D]	AA [auth A] AB [auth D] BA [auth A] BB [auth D] CA [auth B] AA [auth A], AB [auth D], BA [auth A], BB [auth D], CA [auth B], CB [auth D], DA [auth B], DB [auth D], EA [auth B], EB [auth D], FA [auth B], FB [auth D], GA [auth B], GB [auth D], HA [auth B], IA [auth B], IB [auth E], JA [auth B], JB [auth E], KA [auth C], LA [auth C], LB [auth F], MA [auth C], MB [auth F], NA [auth C], OA [auth C], PA [auth C], QA [auth C], RA [auth C], SA [auth C], TA [auth D], UA [auth D], VA [auth D], WA [auth D], XA [auth D], YA [auth D], ZA [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth A] Focus chain AB [auth D] Focus chain BA [auth A] Focus chain BB [auth D] Focus chain CA [auth B] Focus chain CB [auth D] Focus chain DA [auth B] Focus chain DB [auth D] Focus chain EA [auth B] Focus chain EB [auth D] Focus chain FA [auth B] Focus chain FB [auth D] Focus chain GA [auth B] Focus chain GB [auth D] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain IB [auth E] Focus chain JA [auth B] Focus chain JB [auth E] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain LB [auth F] Focus chain MA [auth C] Focus chain MB [auth F] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain TA [auth D] Focus chain UA [auth D] Focus chain VA [auth D] Focus chain WA [auth D] Focus chain XA [auth D] Focus chain YA [auth D] Focus chain ZA [auth D] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth D] Focus chain BA [auth A] Focus chain BB [auth D] Focus chain CA [auth B] Focus chain CB [auth D] Focus chain DA [auth B] Focus chain DB [auth D] Focus chain EA [auth B] Focus chain EB [auth D] Focus chain FA [auth B] Focus chain FB [auth D] Focus chain GA [auth B] Focus chain GB [auth D] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain IB [auth E] Focus chain JA [auth B] Focus chain JB [auth E] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain LB [auth F] Focus chain MA [auth C] Focus chain MB [auth F] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain TA [auth D] Focus chain UA [auth D] Focus chain VA [auth D] Focus chain WA [auth D] Focus chain XA [auth D] Focus chain YA [auth D] Focus chain ZA [auth D]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain HB [auth E] SDF format, chain KB [auth F] SDF format, chain Z [auth A] MOL2 format, chain HB [auth E] MOL2 format, chain KB [auth F] MOL2 format, chain Z [auth A]	HB [auth E], KB [auth F], Z [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain HB [auth E] Focus chain KB [auth F] Focus chain Z [auth A] Interactions & Density Focus chain HB [auth E] Focus chain KB [auth F] Focus chain Z [auth A]