8ZY2

Sarbecovirus BANAL-20-52 Spike Trimer in a Locked Conformation

PDB DOI: https://doi.org/10.2210/pdb8ZY2/pdb
EM Map EMD-60553: EMDB EMDataResource

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

Deposited: 2024-06-16 Released: 2025-02-05
Deposition Author(s): Wang, J., Xiong, X.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.90 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

A locked conformation of spike protein trimer of Sarbecovirus

Wang, J., Xiong, X.

To be published.

Macromolecule Content

Total Structure Weight: 396.04 kDa
Atom Count: 27,099
Modelled Residue Count: 3,309
Deposited Residue Count: 3,408
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 glycoprotein	A, B, C	1,136	Sarbecovirus	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: 18	Glycosylation Focus chain A Focus chain B Focus chain C	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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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, E, F, G, H D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X	2		N-Glycosylation	Interactions Focus chain D Focus chain E 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 Interactions & Density Focus chain D Focus chain E 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
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 3 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 KB [auth C] SDF format, chain XA [auth B] SDF format, chain JA [auth A] MOL2 format, chain KB [auth C] MOL2 format, chain XA [auth B] MOL2 format, chain JA [auth A] mmCIF format, chain KB [auth C] mmCIF format, chain XA [auth B] mmCIF format, chain JA [auth A]	JA [auth A], KB [auth C], XA [auth B]	BILIVERDINE IX ALPHA C₃₃ H₃₄ N₄ O₆ GWZYPXHJIZCRAJ-SRVCBVSDSA-N		Interactions Focus chain JA [auth A] Focus chain KB [auth C] Focus chain XA [auth B] Interactions & Density Focus chain JA [auth A] Focus chain KB [auth C] Focus chain XA [auth B]
EIC Query on EIC Download Ideal Coordinates CCD File SDF format, chain KA [auth A] SDF format, chain LA [auth B] SDF format, chain YA [auth C] MOL2 format, chain KA [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain YA [auth C] mmCIF format, chain KA [auth A] mmCIF format, chain LA [auth B] mmCIF format, chain YA [auth C]	KA [auth A], LA [auth B], YA [auth C]	LINOLEIC ACID C₁₈ H₃₂ O₂ OYHQOLUKZRVURQ-HZJYTTRNSA-N		Interactions Focus chain KA [auth A] Focus chain LA [auth B] Focus chain YA [auth C] Interactions & Density Focus chain KA [auth A] Focus chain LA [auth B] Focus chain YA [auth C]
NAG 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 A] SDF format, chain BB [auth C] SDF format, chain CB [auth C] SDF format, chain DA [auth A] SDF format, chain DB [auth C] SDF format, chain EA [auth A] SDF format, chain EB [auth C] SDF format, chain FA [auth A] SDF format, chain FB [auth C] SDF format, chain GA [auth A] SDF format, chain HA [auth A] SDF format, chain HB [auth C] SDF format, chain IA [auth A] SDF format, chain IB [auth C] SDF format, chain JB [auth C] SDF format, chain MA [auth B] SDF format, chain PA [auth B] SDF format, chain QA [auth B] SDF format, chain SA [auth B] SDF format, chain TA [auth B] SDF format, chain UA [auth B] SDF format, chain VA [auth B] SDF format, chain WA [auth B] SDF format, chain Y [auth A] SDF format, chain Z [auth A] SDF format, chain ZA [auth C] SDF format, chain CA [auth A] SDF format, chain GB [auth C] SDF format, chain NA [auth B] SDF format, chain OA [auth B] SDF format, chain RA [auth B] MOL2 format, chain AA [auth A] MOL2 format, chain AB [auth C] MOL2 format, chain BA [auth A] MOL2 format, chain BB [auth C] MOL2 format, chain CB [auth C] MOL2 format, chain DA [auth A] MOL2 format, chain DB [auth C] MOL2 format, chain EA [auth A] MOL2 format, chain EB [auth C] MOL2 format, chain FA [auth A] MOL2 format, chain FB [auth C] MOL2 format, chain GA [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain HB [auth C] MOL2 format, chain IA [auth A] MOL2 format, chain IB [auth C] MOL2 format, chain JB [auth C] MOL2 format, chain MA [auth B] MOL2 format, chain PA [auth B] MOL2 format, chain QA [auth B] MOL2 format, chain SA [auth B] MOL2 format, chain TA [auth B] MOL2 format, chain UA [auth B] MOL2 format, chain VA [auth B] MOL2 format, chain WA [auth B] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth C] MOL2 format, chain CA [auth A] MOL2 format, chain GB [auth C] MOL2 format, chain NA [auth B] MOL2 format, chain OA [auth B] MOL2 format, chain RA [auth B] mmCIF format, chain AA [auth A] mmCIF format, chain AB [auth C] mmCIF format, chain BA [auth A] mmCIF format, chain BB [auth C] mmCIF format, chain CB [auth C] mmCIF format, chain DA [auth A] mmCIF format, chain DB [auth C] mmCIF format, chain EA [auth A] mmCIF format, chain EB [auth C] mmCIF format, chain FA [auth A] mmCIF format, chain FB [auth C] mmCIF format, chain GA [auth A] mmCIF format, chain HA [auth A] mmCIF format, chain HB [auth C] mmCIF format, chain IA [auth A] mmCIF format, chain IB [auth C] mmCIF format, chain JB [auth C] mmCIF format, chain MA [auth B] mmCIF format, chain PA [auth B] mmCIF format, chain QA [auth B] mmCIF format, chain SA [auth B] mmCIF format, chain TA [auth B] mmCIF format, chain UA [auth B] mmCIF format, chain VA [auth B] mmCIF format, chain WA [auth B] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain ZA [auth C] mmCIF format, chain CA [auth A] mmCIF format, chain GB [auth C] mmCIF format, chain NA [auth B] mmCIF format, chain OA [auth B] mmCIF format, chain RA [auth B]	AA [auth A] AB [auth C] BA [auth A] BB [auth C] CA [auth A] AA [auth A], AB [auth C], BA [auth A], 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 C], IA [auth A], IB [auth C], JB [auth C], MA [auth B], NA [auth B], OA [auth B], PA [auth B], QA [auth B], RA [auth B], SA [auth B], TA [auth B], UA [auth B], VA [auth B], WA [auth B], Y [auth A], Z [auth A], ZA [auth C]	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 A] 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 C] Focus chain IA [auth A] Focus chain IB [auth C] Focus chain JB [auth C] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain UA [auth B] Focus chain VA [auth B] Focus chain WA [auth B] Focus chain Y [auth A] Focus chain Z [auth A] Focus chain ZA [auth C] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth C] Focus chain BA [auth A] 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 C] Focus chain IA [auth A] Focus chain IB [auth C] Focus chain JB [auth C] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain UA [auth B] Focus chain VA [auth B] Focus chain WA [auth B] Focus chain Y [auth A] Focus chain Z [auth A] Focus chain ZA [auth C]