7WGV

SARS-CoV-2 spike glycoprotein trimer in closed state

PDB DOI: https://doi.org/10.2210/pdb7WGV/pdb
EM Map EMD-32490: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2021-12-29 Released: 2023-01-04
Deposition Author(s): Zhu, Y., Tai, L., Yin, G., Sun, F.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.20 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

Novel cleavage sites identified in SARS-CoV-2 spike protein reveal mechanism for cathepsin L-facilitated viral infection and treatment strategies

Zhao, M.M., Zhu, Y., Zhang, L., Zhong, G., Tai, L., Liu, S., Yin, G., Lu, J., He, Q., Li, M.J., Zhao, R.X., Wang, H., Huang, W., Fan, C., Shuai, L., Wen, Z., Wang, C., He, X., Chen, Q., Liu, B., Xiong, X., Bu, Z., Wang, Y., Sun, F., Yang, J.K.

(2022) Cell Discov 8: 53

DOI: https://doi.org/10.1038/s41421-022-00419-w

Macromolecule Content

Total Structure Weight: 417.23 kDa
Atom Count: 26,931
Modelled Residue Count: 3,309
Deposited Residue Count: 3,612
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	1,204	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 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
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, E, F, G, H D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R	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 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
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BLR Query on BLR Download Ideal Coordinates CCD File SDF format, chain EA [auth A] SDF format, chain EB [auth C] SDF format, chain RA [auth B] MOL2 format, chain EA [auth A] MOL2 format, chain EB [auth C] MOL2 format, chain RA [auth B]	EA [auth A], EB [auth C], RA [auth B]	3-[5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-2-[[5-[(Z)-(3-ethenyl-4-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1H-pyrrol-2-yl]methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acid C₃₃ H₃₆ N₄ O₆ BPYKTIZUTYGOLE-IFADSCNNSA-N		Interactions Focus chain EA [auth A] Focus chain EB [auth C] Focus chain RA [auth B] Interactions & Density Focus chain EA [auth A] Focus chain EB [auth C] Focus chain RA [auth B]
EIC Query on EIC Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain AB [auth C] SDF format, chain NA [auth B] MOL2 format, chain AA [auth A] MOL2 format, chain AB [auth C] MOL2 format, chain NA [auth B]	AA [auth A], AB [auth C], NA [auth B]	LINOLEIC ACID C₁₈ H₃₂ O₂ OYHQOLUKZRVURQ-HZJYTTRNSA-N		Interactions Focus chain AA [auth A] Focus chain AB [auth C] Focus chain NA [auth B] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth C] Focus chain NA [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain BA [auth A] 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 DB [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 KA [auth B] SDF format, chain LA [auth B] SDF format, chain MA [auth B] SDF format, chain OA [auth B] SDF format, chain PA [auth B] SDF format, chain QA [auth B] 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 V [auth A] 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] SDF format, chain ZA [auth C] MOL2 format, chain BA [auth A] 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 DB [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 KA [auth B] MOL2 format, chain LA [auth B] MOL2 format, chain MA [auth B] MOL2 format, chain OA [auth B] MOL2 format, chain PA [auth B] MOL2 format, chain QA [auth B] 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 V [auth A] 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] MOL2 format, chain ZA [auth C]	BA [auth A] BB [auth C] CA [auth A] CB [auth C] DA [auth A] BA [auth A], BB [auth C], CA [auth A], CB [auth C], DA [auth A], DB [auth C], FA [auth B], GA [auth B], HA [auth B], IA [auth B], JA [auth B], KA [auth B], LA [auth B], MA [auth B], OA [auth B], PA [auth B], QA [auth B], S [auth A], SA [auth C], T [auth A], TA [auth C], U [auth A], UA [auth C], V [auth A], VA [auth C], W [auth A], WA [auth C], X [auth A], XA [auth C], Y [auth A], YA [auth C], Z [auth A], ZA [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions 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 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 KA [auth B] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain QA [auth B] 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 V [auth A] 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] Focus chain ZA [auth C] Interactions & Density 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 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 KA [auth B] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain QA [auth B] 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 V [auth A] 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] Focus chain ZA [auth C]