8I9B

S-ECD (Omicron BA.2.75) in complex with PD of ACE2

PDB DOI: https://doi.org/10.2210/pdb8I9B/pdb
EM Map EMD-35264: EMDB EMDataResource

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

Deposited: 2023-02-06 Released: 2024-02-07
Deposition Author(s): Li, Y.N., Shen, Y.P., Zhang, Y.Y., Yan, R.H.
Funding Organization(s): Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Cryo-EM structures of SARS-CoV-2 BA.2-derived subvariants spike in complex with ACE2 receptor.

Li, Y., Ren, C., Shen, Y., Zhang, Y., Chen, J., Zheng, J., Tian, R., Cao, L., Yan, R.

(2023) Cell Discov 9: 108-108

PubMed: 37919275 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41421-023-00607-2
Primary Citation of Related Structures:
8I9B, 8I9C, 8I9D, 8I9F, 8I9G, 8I9H

Organizational Affiliation

Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.

Macromolecule Content

Total Structure Weight: 660.93 kDa
Atom Count: 39,539
Modelled Residue Count: 4,786
Deposited Residue Count: 5,676
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	1,268	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 44 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: 16	Glycosylation Focus chain A Focus chain B Focus chain C	Go to GlyGen: P0DTC2-1
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 [auth F], E [auth D], F [auth E]	624	Homo sapiens	Mutation(s): 0 Gene Names: ACE2, UNQ868/PRO1885 EC: 3.4.17 (UniProt), 3.4.17.23 (UniProt)
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
Glycosylation
Glycosylation Sites: 6	Glycosylation Focus chain D [auth F] Focus chain E [auth D] Focus chain F [auth E]	Go to GlyGen: Q9BYF1-1
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], EA [auth e], AA [auth a], BA [auth b], CA [auth c], DA [auth d], EA [auth e], FA [auth f], G, GA [auth g], H, HA [auth h], I, IA [auth i], J, JA [auth j], K, KA [auth k], L, LA [auth l], M, MA [auth m], N, NA [auth n], O, OA [auth o], P, PA [auth p], Q, QA [auth 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 EA [auth e] Focus chain FA [auth f] Focus chain G Focus chain GA [auth g] Focus chain H Focus chain HA [auth h] Focus chain I Focus chain IA [auth i] Focus chain J Focus chain JA [auth j] Focus chain K Focus chain KA [auth k] Focus chain L Focus chain LA [auth l] Focus chain M Focus chain MA [auth m] Focus chain N Focus chain NA [auth n] Focus chain O Focus chain OA [auth o] Focus chain P Focus chain PA [auth p] Focus chain Q Focus chain QA [auth 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 EA [auth e] Focus chain FA [auth f] Focus chain G Focus chain GA [auth g] Focus chain H Focus chain HA [auth h] Focus chain I Focus chain IA [auth i] Focus chain J Focus chain JA [auth j] Focus chain K Focus chain KA [auth k] Focus chain L Focus chain LA [auth l] Focus chain M Focus chain MA [auth m] Focus chain N Focus chain NA [auth n] Focus chain O Focus chain OA [auth o] Focus chain P Focus chain PA [auth p] Focus chain Q Focus chain QA [auth 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 (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain DB [auth B] SDF format, chain HB [auth B] SDF format, chain IB [auth B] SDF format, chain LB [auth C] SDF format, chain OB [auth C] SDF format, chain PB [auth C] SDF format, chain RB [auth F] SDF format, chain UA [auth A] SDF format, chain WA [auth A] SDF format, chain YA [auth A] SDF format, chain AB [auth A] SDF format, chain BB [auth B] SDF format, chain CB [auth B] SDF format, chain EB [auth B] SDF format, chain FB [auth B] SDF format, chain GB [auth B] SDF format, chain JB [auth C] SDF format, chain KB [auth C] SDF format, chain MB [auth C] SDF format, chain NB [auth C] SDF format, chain QB [auth C] SDF format, chain RA [auth A] SDF format, chain SA [auth A] SDF format, chain SB [auth D] SDF format, chain TA [auth A] SDF format, chain TB [auth E] SDF format, chain VA [auth A] SDF format, chain XA [auth A] SDF format, chain ZA [auth A] MOL2 format, chain DB [auth B] MOL2 format, chain HB [auth B] MOL2 format, chain IB [auth B] MOL2 format, chain LB [auth C] MOL2 format, chain OB [auth C] MOL2 format, chain PB [auth C] MOL2 format, chain RB [auth F] MOL2 format, chain UA [auth A] MOL2 format, chain WA [auth A] MOL2 format, chain YA [auth A] MOL2 format, chain AB [auth A] MOL2 format, chain BB [auth B] MOL2 format, chain CB [auth B] MOL2 format, chain EB [auth B] MOL2 format, chain FB [auth B] MOL2 format, chain GB [auth B] MOL2 format, chain JB [auth C] MOL2 format, chain KB [auth C] MOL2 format, chain MB [auth C] MOL2 format, chain NB [auth C] MOL2 format, chain QB [auth C] MOL2 format, chain RA [auth A] MOL2 format, chain SA [auth A] MOL2 format, chain SB [auth D] MOL2 format, chain TA [auth A] MOL2 format, chain TB [auth E] MOL2 format, chain VA [auth A] MOL2 format, chain XA [auth A] MOL2 format, chain ZA [auth A] mmCIF format, chain DB [auth B] mmCIF format, chain HB [auth B] mmCIF format, chain IB [auth B] mmCIF format, chain LB [auth C] mmCIF format, chain OB [auth C] mmCIF format, chain PB [auth C] mmCIF format, chain RB [auth F] mmCIF format, chain UA [auth A] mmCIF format, chain WA [auth A] mmCIF format, chain YA [auth A] mmCIF format, chain AB [auth A] mmCIF format, chain BB [auth B] mmCIF format, chain CB [auth B] mmCIF format, chain EB [auth B] mmCIF format, chain FB [auth B] mmCIF format, chain GB [auth B] mmCIF format, chain JB [auth C] mmCIF format, chain KB [auth C] mmCIF format, chain MB [auth C] mmCIF format, chain NB [auth C] mmCIF format, chain QB [auth C] mmCIF format, chain RA [auth A] mmCIF format, chain SA [auth A] mmCIF format, chain SB [auth D] mmCIF format, chain TA [auth A] mmCIF format, chain TB [auth E] mmCIF format, chain VA [auth A] mmCIF format, chain XA [auth A] mmCIF format, chain ZA [auth A]	AB [auth A] BB [auth B] CB [auth B] DB [auth B] EB [auth B] AB [auth A], BB [auth B], CB [auth B], DB [auth B], EB [auth B], FB [auth B], GB [auth B], HB [auth B], IB [auth B], JB [auth C], KB [auth C], LB [auth C], MB [auth C], NB [auth C], OB [auth C], PB [auth C], QB [auth C], RA [auth A], RB [auth F], SA [auth A], SB [auth D], TA [auth A], TB [auth E], UA [auth A], VA [auth A], WA [auth A], XA [auth A], YA [auth A], ZA [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth A] Focus chain BB [auth B] Focus chain CB [auth B] Focus chain DB [auth B] Focus chain EB [auth B] Focus chain FB [auth B] Focus chain GB [auth B] Focus chain HB [auth B] Focus chain IB [auth B] Focus chain JB [auth C] Focus chain KB [auth C] Focus chain LB [auth C] Focus chain MB [auth C] Focus chain NB [auth C] Focus chain OB [auth C] Focus chain PB [auth C] Focus chain QB [auth C] Focus chain RA [auth A] Focus chain RB [auth F] Focus chain SA [auth A] Focus chain SB [auth D] Focus chain TA [auth A] Focus chain TB [auth E] Focus chain UA [auth A] Focus chain VA [auth A] Focus chain WA [auth A] Focus chain XA [auth A] Focus chain YA [auth A] Focus chain ZA [auth A] Interactions & Density Focus chain AB [auth A] Focus chain BB [auth B] Focus chain CB [auth B] Focus chain DB [auth B] Focus chain EB [auth B] Focus chain FB [auth B] Focus chain GB [auth B] Focus chain HB [auth B] Focus chain IB [auth B] Focus chain JB [auth C] Focus chain KB [auth C] Focus chain LB [auth C] Focus chain MB [auth C] Focus chain NB [auth C] Focus chain OB [auth C] Focus chain PB [auth C] Focus chain QB [auth C] Focus chain RA [auth A] Focus chain RB [auth F] Focus chain SA [auth A] Focus chain SB [auth D] Focus chain TA [auth A] Focus chain TB [auth E] Focus chain UA [auth A] Focus chain VA [auth A] Focus chain WA [auth A] Focus chain XA [auth A] Focus chain YA [auth A] Focus chain ZA [auth A]