7YBI

SARS-CoV-2 Mu variant spike (open state)

PDB DOI: https://doi.org/10.2210/pdb7YBI/pdb
EM Map EMD-33722: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2022-06-29 Released: 2023-07-12
Deposition Author(s): Wang, X., Fu, W.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.10 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

SARS-CoV-2 lambda variant spike

Wang, X., Fu, W.

To be published.

Macromolecule Content

Total Structure Weight: 443.48 kDa
Atom Count: 26,649
Modelled Residue Count: 3,241
Deposited Residue Count: 3,819
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	1,273	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 9 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	AA [auth a], BA [auth b], CA [auth c], D, E, AA [auth a], BA [auth b], CA [auth c], D, E, F, G, H, L, M, N, O, P, Q, R, V, W, X, Y, Z	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain BA [auth b] Focus chain CA [auth c] Focus chain D Focus chain E Focus chain F Focus chain G Focus chain H Focus chain L Focus chain M Focus chain N Focus chain O Focus chain P Focus chain Q Focus chain R Focus chain V Focus chain W Focus chain X Focus chain Y Focus chain Z Interactions & Density Focus chain AA [auth a] Focus chain BA [auth b] Focus chain CA [auth c] Focus chain D Focus chain E Focus chain F Focus chain G Focus chain H Focus chain L Focus chain M Focus chain N Focus chain O Focus chain P Focus chain Q Focus chain R Focus chain V Focus chain W Focus chain X Focus chain Y Focus chain Z
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	DA [auth d], I, S	3		N-Glycosylation	Interactions Focus chain DA [auth d] Focus chain I Focus chain S Interactions & Density Focus chain DA [auth d] Focus chain I Focus chain S
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	EA [auth e], FA [auth f], J, K, T, EA [auth e], FA [auth f], J, K, T, U	3		N-Glycosylation	Interactions Focus chain EA [auth e] Focus chain FA [auth f] Focus chain J Focus chain K Focus chain T Focus chain U Interactions & Density Focus chain EA [auth e] Focus chain FA [auth f] Focus chain J Focus chain K Focus chain T Focus chain U
Glycosylation Resources
GlyTouCan: G62182OO GlyCosmos: G62182OO GlyGen: G62182OO

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 EB [auth C] SDF format, chain HA [auth A] SDF format, chain IA [auth A] SDF format, chain KA [auth A] SDF format, chain LA [auth A] SDF format, chain NA [auth A] SDF format, chain TA [auth B] SDF format, chain UA [auth B] SDF format, chain WA [auth B] SDF format, chain YA [auth B] SDF format, chain ZA [auth B] SDF format, chain AB [auth C] SDF format, chain BB [auth C] SDF format, chain CB [auth C] SDF format, chain DB [auth C] SDF format, chain FB [auth C] SDF format, chain GA [auth A] SDF format, chain GB [auth C] SDF format, chain HB [auth C] SDF format, chain JA [auth A] SDF format, chain MA [auth A] SDF format, chain OA [auth A] SDF format, chain PA [auth A] SDF format, chain QA [auth A] SDF format, chain RA [auth B] SDF format, chain SA [auth B] SDF format, chain VA [auth B] SDF format, chain XA [auth B] MOL2 format, chain EB [auth C] MOL2 format, chain HA [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain KA [auth A] MOL2 format, chain LA [auth A] MOL2 format, chain NA [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain UA [auth B] MOL2 format, chain WA [auth B] MOL2 format, chain YA [auth B] MOL2 format, chain ZA [auth B] MOL2 format, chain AB [auth C] MOL2 format, chain BB [auth C] MOL2 format, chain CB [auth C] MOL2 format, chain DB [auth C] MOL2 format, chain FB [auth C] MOL2 format, chain GA [auth A] MOL2 format, chain GB [auth C] MOL2 format, chain HB [auth C] MOL2 format, chain JA [auth A] MOL2 format, chain MA [auth A] MOL2 format, chain OA [auth A] MOL2 format, chain PA [auth A] MOL2 format, chain QA [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain SA [auth B] MOL2 format, chain VA [auth B] MOL2 format, chain XA [auth B]	AB [auth C] BB [auth C] CB [auth C] DB [auth C] EB [auth C] AB [auth C], BB [auth C], CB [auth C], DB [auth C], EB [auth C], FB [auth C], GA [auth A], GB [auth C], HA [auth A], HB [auth C], IA [auth A], JA [auth A], KA [auth A], LA [auth A], MA [auth A], NA [auth A], OA [auth A], PA [auth A], QA [auth A], RA [auth B], SA [auth B], TA [auth B], UA [auth B], VA [auth B], WA [auth B], XA [auth B], YA [auth B], ZA [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth C] Focus chain BB [auth C] Focus chain CB [auth C] Focus chain DB [auth C] Focus chain EB [auth C] 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 JA [auth A] Focus chain KA [auth A] Focus chain LA [auth A] Focus chain MA [auth A] Focus chain NA [auth A] Focus chain OA [auth A] Focus chain PA [auth A] Focus chain QA [auth A] 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 XA [auth B] Focus chain YA [auth B] Focus chain ZA [auth B] Interactions & Density Focus chain AB [auth C] Focus chain BB [auth C] Focus chain CB [auth C] Focus chain DB [auth C] Focus chain EB [auth C] 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 JA [auth A] Focus chain KA [auth A] Focus chain LA [auth A] Focus chain MA [auth A] Focus chain NA [auth A] Focus chain OA [auth A] Focus chain PA [auth A] Focus chain QA [auth A] 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 XA [auth B] Focus chain YA [auth B] Focus chain ZA [auth B]