9W76 | pdb_00009w76

sarbecovirus Rc-o319 S-trimer in a locked-2 conformation

PDB DOI: https://doi.org/10.2210/pdb9W76/pdb
EM Map EMD-65718: EMDB EMDataResource

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

Deposited: 2025-08-05 Released: 2025-10-29
Deposition Author(s): Wang, J., Li, Z.X., Li, Z.M., Huang, Y., Xiong, X.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.30 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

sarbecovirus Rc-o319 S-trimer in a locked-2 conformation

Wang, J., Li, Z., Li, Z.M., Yuan, H., Xiong, X.

To be published.

Macromolecule Content

Total Structure Weight: 432.63 kDa
Atom Count: 26,232
Modeled Residue Count: 3,231
Deposited Residue Count: 3,762
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A, B, C	1,254	Sarbecovirus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 17	Glycosylation Focus chain A Focus chain B Focus chain C
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, G, J	4		N-Glycosylation	Interactions Focus chain D Focus chain G Focus chain J Interactions & Density Focus chain D Focus chain G Focus chain J
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

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	E, F, H, I, K E, F, H, I, K, L	2		N-Glycosylation	Interactions Focus chain E Focus chain F Focus chain H Focus chain I Focus chain K Focus chain L Interactions & Density Focus chain E Focus chain F Focus chain H Focus chain I Focus chain K Focus chain L
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BLA (Subject of Investigation/LOI) Query on BLA Download Ideal Coordinates CCD File SDF format, chain KA [auth B] SDF format, chain V [auth A] SDF format, chain ZA [auth C] MOL2 format, chain KA [auth B] MOL2 format, chain V [auth A] MOL2 format, chain ZA [auth C] mmCIF format, chain KA [auth B] mmCIF format, chain V [auth A] mmCIF format, chain ZA [auth C]	KA [auth B], V [auth A], ZA [auth C]	BILIVERDINE IX ALPHA C₃₃ H₃₄ N₄ O₆ GWZYPXHJIZCRAJ-SRVCBVSDSA-N		Interactions Focus chain KA [auth B] Focus chain V [auth A] Focus chain ZA [auth C] Interactions & Density Focus chain KA [auth B] Focus chain V [auth A] Focus chain ZA [auth C]
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain AB [auth C] SDF format, chain BA [auth B] SDF format, chain BB [auth C] SDF format, chain CA [auth B] SDF format, chain CB [auth C] SDF format, chain DA [auth B] SDF format, chain DB [auth C] SDF format, chain EA [auth B] SDF format, chain EB [auth C] SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain HA [auth B] SDF format, chain IA [auth B] SDF format, chain JA [auth B] SDF format, chain LA [auth B] SDF format, chain M [auth A] SDF format, chain MA [auth B] SDF format, chain N [auth A] SDF format, chain NA [auth B] SDF format, chain O [auth A] SDF format, chain OA [auth B] SDF format, chain P [auth A] SDF format, chain PA [auth B] SDF format, chain Q [auth A] SDF format, chain QA [auth C] SDF format, chain R [auth A] SDF format, chain RA [auth C] SDF format, chain S [auth A] SDF format, chain SA [auth C] SDF format, chain T [auth A] SDF format, chain TA [auth C] SDF format, chain U [auth A] SDF format, chain UA [auth C] SDF format, chain VA [auth C] SDF format, chain W [auth A] SDF format, chain WA [auth C] SDF format, chain X [auth A] SDF format, chain XA [auth C] SDF format, chain Y [auth A] SDF format, chain YA [auth C] SDF format, chain Z [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain AB [auth C] MOL2 format, chain BA [auth B] MOL2 format, chain BB [auth C] MOL2 format, chain CA [auth B] MOL2 format, chain CB [auth C] MOL2 format, chain DA [auth B] MOL2 format, chain DB [auth C] MOL2 format, chain EA [auth B] MOL2 format, chain EB [auth C] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain LA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth C] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth C] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth C] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth C] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth C] MOL2 format, chain VA [auth C] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth C] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth C] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth C] MOL2 format, chain Z [auth A] mmCIF format, chain AA [auth A] mmCIF format, chain AB [auth C] mmCIF format, chain BA [auth B] mmCIF format, chain BB [auth C] mmCIF format, chain CA [auth B] mmCIF format, chain CB [auth C] mmCIF format, chain DA [auth B] mmCIF format, chain DB [auth C] mmCIF format, chain EA [auth B] mmCIF format, chain EB [auth C] mmCIF format, chain FA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain IA [auth B] mmCIF format, chain JA [auth B] mmCIF format, chain LA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth B] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth C] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth C] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth C] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth C] mmCIF format, chain U [auth A] mmCIF format, chain UA [auth C] mmCIF format, chain VA [auth C] mmCIF format, chain W [auth A] mmCIF format, chain WA [auth C] mmCIF format, chain X [auth A] mmCIF format, chain XA [auth C] mmCIF format, chain Y [auth A] mmCIF format, chain YA [auth C] mmCIF format, chain Z [auth A]	AA [auth A] AB [auth C] BA [auth B] BB [auth C] CA [auth B] AA [auth A], AB [auth C], BA [auth B], BB [auth C], CA [auth B], CB [auth C], DA [auth B], DB [auth C], EA [auth B], EB [auth C], FA [auth B], GA [auth B], HA [auth B], IA [auth B], JA [auth B], LA [auth B], M [auth A], MA [auth B], N [auth A], NA [auth B], O [auth A], OA [auth B], P [auth A], PA [auth B], Q [auth A], QA [auth C], R [auth A], RA [auth C], S [auth A], SA [auth C], T [auth A], TA [auth C], U [auth A], UA [auth C], VA [auth C], W [auth A], WA [auth C], X [auth A], XA [auth C], Y [auth A], YA [auth C], Z [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth A] Focus chain AB [auth C] Focus chain BA [auth B] Focus chain BB [auth C] Focus chain CA [auth B] Focus chain CB [auth C] Focus chain DA [auth B] Focus chain DB [auth C] Focus chain EA [auth B] Focus chain EB [auth C] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain R [auth A] Focus chain RA [auth C] Focus chain S [auth A] Focus chain SA [auth C] Focus chain T [auth A] Focus chain TA [auth C] Focus chain U [auth A] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain W [auth A] Focus chain WA [auth C] Focus chain X [auth A] Focus chain XA [auth C] Focus chain Y [auth A] Focus chain YA [auth C] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth C] Focus chain BA [auth B] Focus chain BB [auth C] Focus chain CA [auth B] Focus chain CB [auth C] Focus chain DA [auth B] Focus chain DB [auth C] Focus chain EA [auth B] Focus chain EB [auth C] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain R [auth A] Focus chain RA [auth C] Focus chain S [auth A] Focus chain SA [auth C] Focus chain T [auth A] Focus chain TA [auth C] Focus chain U [auth A] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain W [auth A] Focus chain WA [auth C] Focus chain X [auth A] Focus chain XA [auth C] Focus chain Y [auth A] Focus chain YA [auth C] Focus chain Z [auth A]