9VG7 | pdb_00009vg7

Cryo-EM Structure of Rc-o319 Ectodomain trimer

PDB DOI: https://doi.org/10.2210/pdb9VG7/pdb
EM Map EMD-65045: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2025-06-13 Released: 2025-08-27
Deposition Author(s): Matsumoto, K., Shihoya, W., Nureki, O.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.55 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

Molecular basis of sarbecovirus evolution and receptor tropism in natural hosts, potential intermediate hosts, and humans.

Kosugi, Y., Matsumoto, K., Lytras, S., Plianchaisuk, A., Tolentino, J.E., Fujita, S., Yo, M.S., Luo, C., Kim, Y., Shihoya, W., Ito, J., Nureki, O., Sato, K.

(2025) Cell Rep 44: 116220-116220

PubMed: 40934083 Search on PubMed
DOI: https://doi.org/10.1016/j.celrep.2025.116220
Primary Citation of Related Structures:
9M3F, 9VG7

PubMed Abstract:
The spike protein of many sarbecoviruses binds to the angiotensin-converting enzyme 2 (ACE2) receptor and facilitates viral entry. The diversification of the sarbecovirus spike gene and the mammalian ACE2 gene suggests that sarbecoviruses and their hosts have co-evolved, and the genetic diversity in these genes affects the host tropism of sarbecoviruses. Better comprehending the evolutionary potential of sarbecoviruses can lead to preparedness for the next pandemic. However, the host tropism of sarbecoviruses is not fully understood. Here, we performed pseudovirus infection assays using 53 sarbecoviruses and ACE2s from 17 mammals to elucidate the ACE2 tropism of sarbecoviruses in natural hosts, potential intermediate hosts, and humans. We determined the factors responsible for the ACE2 tropism of sarbecoviruses through structural and phylogenetic analyses and infection experiments, revealing which substitutions can expand the host range of sarbecoviruses. These results highlight the mechanisms modulating host tropism throughout sarbecovirus evolution.

Organizational Affiliation

Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.

Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK.

Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.

Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.

Department of Life Sciences, Faculty of Natural Science, Imperial College London, London, UK.

Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.

Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan; International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Collaboration Unit for Infection, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan; Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore. Electronic address: keisato@g.ecc.u-tokyo.ac.jp.

Macromolecule Content

Total Structure Weight: 396.26 kDa
Atom Count: 25,665
Modeled Residue Count: 3,225
Deposited Residue Count: 3,501
Unique protein chains: 1

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	1,167	Homo sapiens	Mutation(s): 0
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: 7	Glycosylation Focus chain A Focus chain B Focus chain C	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, F, G, H, J D, F, G, H, J, K, L, N, O	2		N-Glycosylation	Interactions Focus chain D Focus chain F Focus chain G Focus chain H Focus chain J Focus chain K Focus chain L Focus chain N Focus chain O Interactions & Density Focus chain D Focus chain F Focus chain G Focus chain H Focus chain J Focus chain K Focus chain L Focus chain N Focus chain O
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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	E, I, M	3		N-Glycosylation	Interactions Focus chain E Focus chain I Focus chain M Interactions & Density Focus chain E Focus chain I Focus chain M
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

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 P [auth A] SDF format, chain V [auth C] SDF format, chain X [auth C] SDF format, chain W [auth C] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain R [auth A] SDF format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain V [auth C] MOL2 format, chain X [auth C] MOL2 format, chain W [auth C] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain V [auth C] mmCIF format, chain X [auth C] mmCIF format, chain W [auth C] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A]	P [auth A] Q [auth A] R [auth A] S [auth B] T [auth B] P [auth A], Q [auth A], R [auth A], S [auth B], T [auth B], U [auth B], V [auth C], W [auth C], X [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C]