8VKO

Cryo-EM structure of SARS-CoV-2 XBB.1.5 spike protein in complex with human ACE2

PDB DOI: https://doi.org/10.2210/pdb8VKO/pdb
EM Map EMD-43324: EMDB EMDataResource

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2024-01-09 Released: 2024-02-14
Deposition Author(s): Zhu, X., Mannar, D., Saville, J., Poloni, C., Bezeruk, A., Tidey, K., Ahmed, S., Tuttle, K., Vahdatihassani, F., Cholak, S., Cook, L., Steiner, T.S., Subramaniam, S.
Funding Organization(s): Canada Excellence Research Chair Award

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.68 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

SARS-CoV-2 XBB.1.5 Spike Protein: Altered Receptor Binding, Antibody Evasion, and Retention of T Cell Recognition

Mannar, D., Saville, J., Poloni, C., Zhu, X., Bezeruk, A., Tidey, K., Ahmed, S., Tuttle, K., Vahdatihassani, F., Cholak, S., Cook, L., Steiner, T.S., Subramaniam, S.

To be published.

Macromolecule Content

Total Structure Weight: 655.33 kDa
Atom Count: 40,293
Modelled Residue Count: 4,926
Deposited Residue Count: 5,670
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1,284	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 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

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Processed angiotensin-converting enzyme 2	D, E, F	606	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

Help

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	AA [auth a], BA [auth b], CA [auth c], DA [auth d], G, AA [auth a], BA [auth b], CA [auth c], DA [auth d], G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain BA [auth b] Focus chain CA [auth c] Focus chain DA [auth d] Focus chain G Focus chain H 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 R Focus chain S Focus chain T Focus chain U Focus chain V Focus chain W Focus chain X Focus chain Y Focus chain Z Interactions & Density Focus chain AA [auth a] Focus chain BA [auth b] Focus chain CA [auth c] Focus chain DA [auth d] Focus chain G Focus chain H 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 R Focus chain S Focus chain T Focus chain U Focus chain V Focus chain W Focus chain X Focus chain Y Focus chain Z
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AB [auth D] SDF format, chain BB [auth D] SDF format, chain CB [auth D] SDF format, chain DB [auth E] SDF format, chain EA [auth A] SDF format, chain EB [auth E] SDF format, chain FA [auth A] SDF format, chain FB [auth E] SDF format, chain GA [auth A] SDF format, chain GB [auth E] SDF format, chain HA [auth A] SDF format, chain HB [auth F] SDF format, chain IA [auth A] SDF format, chain IB [auth F] SDF format, chain JA [auth A] SDF format, chain JB [auth F] SDF format, chain KA [auth A] SDF format, chain KB [auth F] SDF format, chain LA [auth B] SDF format, chain MA [auth B] SDF format, chain NA [auth B] SDF format, chain OA [auth B] SDF format, chain PA [auth B] SDF format, chain QA [auth B] SDF format, chain RA [auth B] SDF format, chain SA [auth C] SDF format, chain TA [auth C] SDF format, chain UA [auth C] SDF format, chain VA [auth C] SDF format, chain WA [auth C] SDF format, chain XA [auth C] SDF format, chain YA [auth C] SDF format, chain ZA [auth D] MOL2 format, chain AB [auth D] MOL2 format, chain BB [auth D] MOL2 format, chain CB [auth D] MOL2 format, chain DB [auth E] MOL2 format, chain EA [auth A] MOL2 format, chain EB [auth E] MOL2 format, chain FA [auth A] MOL2 format, chain FB [auth E] MOL2 format, chain GA [auth A] MOL2 format, chain GB [auth E] MOL2 format, chain HA [auth A] MOL2 format, chain HB [auth F] MOL2 format, chain IA [auth A] MOL2 format, chain IB [auth F] MOL2 format, chain JA [auth A] MOL2 format, chain JB [auth F] MOL2 format, chain KA [auth A] MOL2 format, chain KB [auth F] MOL2 format, chain LA [auth B] MOL2 format, chain MA [auth B] MOL2 format, chain NA [auth B] MOL2 format, chain OA [auth B] MOL2 format, chain PA [auth B] MOL2 format, chain QA [auth B] MOL2 format, chain RA [auth B] MOL2 format, chain SA [auth C] MOL2 format, chain TA [auth C] MOL2 format, chain UA [auth C] MOL2 format, chain VA [auth C] MOL2 format, chain WA [auth C] MOL2 format, chain XA [auth C] MOL2 format, chain YA [auth C] MOL2 format, chain ZA [auth D]	AB [auth D] BB [auth D] CB [auth D] DB [auth E] EA [auth A] AB [auth D], BB [auth D], CB [auth D], DB [auth E], EA [auth A], EB [auth E], FA [auth A], FB [auth E], GA [auth A], GB [auth E], HA [auth A], HB [auth F], IA [auth A], IB [auth F], JA [auth A], JB [auth F], KA [auth A], KB [auth F], LA [auth B], MA [auth B], NA [auth B], OA [auth B], PA [auth B], QA [auth B], RA [auth B], SA [auth C], TA [auth C], UA [auth C], VA [auth C], WA [auth C], XA [auth C], YA [auth C], ZA [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth D] Focus chain BB [auth D] Focus chain CB [auth D] Focus chain DB [auth E] Focus chain EA [auth A] Focus chain EB [auth E] Focus chain FA [auth A] Focus chain FB [auth E] Focus chain GA [auth A] Focus chain GB [auth E] Focus chain HA [auth A] Focus chain HB [auth F] Focus chain IA [auth A] Focus chain IB [auth F] Focus chain JA [auth A] Focus chain JB [auth F] Focus chain KA [auth A] Focus chain KB [auth F] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth D] Interactions & Density Focus chain AB [auth D] Focus chain BB [auth D] Focus chain CB [auth D] Focus chain DB [auth E] Focus chain EA [auth A] Focus chain EB [auth E] Focus chain FA [auth A] Focus chain FB [auth E] Focus chain GA [auth A] Focus chain GB [auth E] Focus chain HA [auth A] Focus chain HB [auth F] Focus chain IA [auth A] Focus chain IB [auth F] Focus chain JA [auth A] Focus chain JB [auth F] Focus chain KA [auth A] Focus chain KB [auth F] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth D]