8I9H

S-RBD (Omicron XBB.1) in complex with PD of ACE2

PDB DOI: https://doi.org/10.2210/pdb8I9H/pdb
EM Map EMD-35272: EMDB EMDataResource

Classification: HYDROLASE/VIRAL PROTEIN
Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
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: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 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: 98.96 kDa
Atom Count: 6,514
Modelled Residue Count: 780
Deposited Residue Count: 839
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Processed angiotensin-converting enzyme 2	A	616	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
Glycosylation
Glycosylation Sites: 6	Glycosylation Focus chain A	Go to GlyGen: Q9BYF1-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S2'	B [auth E]	223	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 22 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: 1	Glycosylation Focus chain B [auth E]	Go to GlyGen: P0DTC2-1
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	C [auth B], D [auth C], E [auth D], F, G, C [auth B], D [auth C], E [auth D], F, G, H	2		N-Glycosylation	Interactions Focus chain C [auth B] Focus chain D [auth C] Focus chain E [auth D] Focus chain F Focus chain G Focus chain H Interactions & Density Focus chain C [auth B] Focus chain D [auth C] Focus chain E [auth D] Focus chain F Focus chain G Focus chain H
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 I [auth A] MOL2 format, chain I [auth A]	I [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]