7XID | pdb_00007xid

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

PDB DOI: https://doi.org/10.2210/pdb7XID/pdb
EM Map EMD-33203: EMDB EMDataResource

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

Deposited: 2022-04-12 Released: 2022-06-15
Deposition Author(s): Li, Y.N., Shen, Y.P., Zhang, Y.Y., Yan, R.H.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.30 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

Structural and functional analysis of an inter-Spike bivalent neutralizing antibody against SARS-CoV-2 variants.

Li, Y., Fan, Q., Zhou, B., Shen, Y., Zhang, Y., Cheng, L., Qi, F., Song, S., Guo, Y., Yan, R., Ju, B., Zhang, Z.

(2022) iScience 25: 104431-104431

PubMed: 35607524 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.isci.2022.104431
Primary Citation Related Structures:
7XIC, 7XID

PubMed Abstract:
The different variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have attracted most public concern because they caused "wave and wave" COVID-19 pandemic. The initial step of viral infection is mediated by the SARS-CoV-2 Spike (S) protein, which mediates the receptor recognition and membrane fusion between virus and host cells. Neutralizing antibodies (nAbs) targeting the S protein of SARS-CoV-2 have become promising candidates for clinical intervention strategy, while multiple studies have shown that different variants have enhanced infectivity and antibody resistance. Here, we explore the structure and function of STS165, a broadly inter-Spike bivalent nAb against SARS-CoV-2 variants and even SARS-CoV, contributing to further understanding of the working mechanism of nAbs.

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, Zhejiang Province, Hangzhou 310024, China.

Macromolecule Content

Total Structure Weight: 630.54 kDa
Atom Count: 34,256
Modeled Residue Count: 4,153
Deposited Residue Count: 5,435
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1,267	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Angiotensin-converting enzyme 2	D, E	817	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
PHAROS: Q9BYF1 GTEx: ENSG00000130234
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9BYF1
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain D Focus chain E	Go to GlyGen: Q9BYF1-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a], BA [auth b], F, G, H, AA [auth a], BA [auth b], F, 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 F 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 F 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 (Subject of Investigation/LOI) Query on NAG Download:Ideal Coordinates CCD File SDF format, chain BB [auth C] SDF format, chain CA [auth A] SDF format, chain CB [auth C] SDF format, chain DA [auth A] SDF format, chain EA [auth A] SDF format, chain EB [auth C] SDF format, chain HA [auth A] SDF format, chain IA [auth A] SDF format, chain IB [auth D] SDF format, chain JA [auth A] SDF format, chain JB [auth D] SDF format, chain LA [auth A] SDF format, chain LB [auth D] SDF format, chain NB [auth D] SDF format, chain OB [auth E] SDF format, chain PA [auth B] SDF format, chain QA [auth B] SDF format, chain QB [auth E] SDF format, chain SA [auth B] SDF format, chain SB [auth E] SDF format, chain TA [auth B] SDF format, chain UA [auth B] SDF format, chain UB [auth E] SDF format, chain VA [auth B] SDF format, chain WA [auth B] SDF format, chain YA [auth C] SDF format, chain ZA [auth C] SDF format, chain XA [auth B] SDF format, chain TB [auth E] SDF format, chain RB [auth E] SDF format, chain RA [auth B] SDF format, chain PB [auth E] SDF format, chain OA [auth B] SDF format, chain NA [auth B] SDF format, chain MB [auth D] SDF format, chain MA [auth A] SDF format, chain KB [auth D] SDF format, chain KA [auth A] SDF format, chain HB [auth D] SDF format, chain GB [auth C] SDF format, chain GA [auth A] SDF format, chain FB [auth C] SDF format, chain FA [auth A] SDF format, chain DB [auth C] SDF format, chain AB [auth C] MOL2 format, chain BB [auth C] MOL2 format, chain CA [auth A] MOL2 format, chain CB [auth C] MOL2 format, chain DA [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain EB [auth C] MOL2 format, chain HA [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain IB [auth D] MOL2 format, chain JA [auth A] MOL2 format, chain JB [auth D] MOL2 format, chain LA [auth A] MOL2 format, chain LB [auth D] MOL2 format, chain NB [auth D] MOL2 format, chain OB [auth E] MOL2 format, chain PA [auth B] MOL2 format, chain QA [auth B] MOL2 format, chain QB [auth E] MOL2 format, chain SA [auth B] MOL2 format, chain SB [auth E] MOL2 format, chain TA [auth B] MOL2 format, chain UA [auth B] MOL2 format, chain UB [auth E] MOL2 format, chain VA [auth B] MOL2 format, chain WA [auth B] MOL2 format, chain YA [auth C] MOL2 format, chain ZA [auth C] MOL2 format, chain XA [auth B] MOL2 format, chain TB [auth E] MOL2 format, chain RB [auth E] MOL2 format, chain RA [auth B] MOL2 format, chain PB [auth E] MOL2 format, chain OA [auth B] MOL2 format, chain NA [auth B] MOL2 format, chain MB [auth D] MOL2 format, chain MA [auth A] MOL2 format, chain KB [auth D] MOL2 format, chain KA [auth A] MOL2 format, chain HB [auth D] MOL2 format, chain GB [auth C] MOL2 format, chain GA [auth A] MOL2 format, chain FB [auth C] MOL2 format, chain FA [auth A] MOL2 format, chain DB [auth C] MOL2 format, chain AB [auth C] mmCIF format, chain BB [auth C] mmCIF format, chain CA [auth A] mmCIF format, chain CB [auth C] mmCIF format, chain DA [auth A] mmCIF format, chain EA [auth A] mmCIF format, chain EB [auth C] mmCIF format, chain HA [auth A] mmCIF format, chain IA [auth A] mmCIF format, chain IB [auth D] mmCIF format, chain JA [auth A] mmCIF format, chain JB [auth D] mmCIF format, chain LA [auth A] mmCIF format, chain LB [auth D] mmCIF format, chain NB [auth D] mmCIF format, chain OB [auth E] mmCIF format, chain PA [auth B] mmCIF format, chain QA [auth B] mmCIF format, chain QB [auth E] mmCIF format, chain SA [auth B] mmCIF format, chain SB [auth E] mmCIF format, chain TA [auth B] mmCIF format, chain UA [auth B] mmCIF format, chain UB [auth E] mmCIF format, chain VA [auth B] mmCIF format, chain WA [auth B] mmCIF format, chain YA [auth C] mmCIF format, chain ZA [auth C] mmCIF format, chain XA [auth B] mmCIF format, chain TB [auth E] mmCIF format, chain RB [auth E] mmCIF format, chain RA [auth B] mmCIF format, chain PB [auth E] mmCIF format, chain OA [auth B] mmCIF format, chain NA [auth B] mmCIF format, chain MB [auth D] mmCIF format, chain MA [auth A] mmCIF format, chain KB [auth D] mmCIF format, chain KA [auth A] mmCIF format, chain HB [auth D] mmCIF format, chain GB [auth C] mmCIF format, chain GA [auth A] mmCIF format, chain FB [auth C] mmCIF format, chain FA [auth A] mmCIF format, chain DB [auth C] mmCIF format, chain AB [auth C]	AB [auth C] BB [auth C] CA [auth A] CB [auth C] DA [auth A] AB [auth C], BB [auth C], CA [auth A], CB [auth C], DA [auth A], DB [auth C], EA [auth A], EB [auth C], FA [auth A], FB [auth C], GA [auth A], GB [auth C], HA [auth A], HB [auth D], IA [auth A], IB [auth D], JA [auth A], JB [auth D], KA [auth A], KB [auth D], LA [auth A], LB [auth D], MA [auth A], MB [auth D], NA [auth B], NB [auth D], OA [auth B], OB [auth E], PA [auth B], PB [auth E], QA [auth B], QB [auth E], RA [auth B], RB [auth E], SA [auth B], SB [auth E], TA [auth B], TB [auth E], UA [auth B], UB [auth E], VA [auth B], WA [auth B], XA [auth B], YA [auth C], ZA [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth C] Focus chain BB [auth C] Focus chain CA [auth A] Focus chain CB [auth C] Focus chain DA [auth A] Focus chain DB [auth C] Focus chain EA [auth A] Focus chain EB [auth C] Focus chain FA [auth A] Focus chain FB [auth C] Focus chain GA [auth A] Focus chain GB [auth C] Focus chain HA [auth A] Focus chain HB [auth D] Focus chain IA [auth A] Focus chain IB [auth D] Focus chain JA [auth A] Focus chain JB [auth D] Focus chain KA [auth A] Focus chain KB [auth D] Focus chain LA [auth A] Focus chain LB [auth D] Focus chain MA [auth A] Focus chain MB [auth D] Focus chain NA [auth B] Focus chain NB [auth D] Focus chain OA [auth B] Focus chain OB [auth E] Focus chain PA [auth B] Focus chain PB [auth E] Focus chain QA [auth B] Focus chain QB [auth E] Focus chain RA [auth B] Focus chain RB [auth E] Focus chain SA [auth B] Focus chain SB [auth E] Focus chain TA [auth B] Focus chain TB [auth E] Focus chain UA [auth B] Focus chain UB [auth E] Focus chain VA [auth B] Focus chain WA [auth B] Focus chain XA [auth B] Focus chain YA [auth C] Focus chain ZA [auth C] Interactions & Density Focus chain AB [auth C] Focus chain BB [auth C] Focus chain CA [auth A] Focus chain CB [auth C] Focus chain DA [auth A] Focus chain DB [auth C] Focus chain EA [auth A] Focus chain EB [auth C] Focus chain FA [auth A] Focus chain FB [auth C] Focus chain GA [auth A] Focus chain GB [auth C] Focus chain HA [auth A] Focus chain HB [auth D] Focus chain IA [auth A] Focus chain IB [auth D] Focus chain JA [auth A] Focus chain JB [auth D] Focus chain KA [auth A] Focus chain KB [auth D] Focus chain LA [auth A] Focus chain LB [auth D] Focus chain MA [auth A] Focus chain MB [auth D] Focus chain NA [auth B] Focus chain NB [auth D] Focus chain OA [auth B] Focus chain OB [auth E] Focus chain PA [auth B] Focus chain PB [auth E] Focus chain QA [auth B] Focus chain QB [auth E] Focus chain RA [auth B] Focus chain RB [auth E] Focus chain SA [auth B] Focus chain SB [auth E] Focus chain TA [auth B] Focus chain TB [auth E] Focus chain UA [auth B] Focus chain UB [auth E] Focus chain VA [auth B] Focus chain WA [auth B] Focus chain XA [auth B] Focus chain YA [auth C] Focus chain ZA [auth C]