7Z3Z

Locked Wuhan SARS-CoV2 Prefusion Spike ectodomain with lipid bound

PDB DOI: https://doi.org/10.2210/pdb7Z3Z/pdb
EM Map EMD-14481: EMDB EMDataResource

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

Deposited: 2022-03-03 Released: 2022-05-04
Deposition Author(s): Duyvesteyn, H.M.E., Carrique, L., Ren, J., Stuart, D.I., Fry, E.E.
Funding Organization(s): CAMS Innovation Fund for Medical Sciences (CIFMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.10 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

The SARS-CoV-2 Spike harbours a lipid binding pocket which modulates stability of the prefusion trimer

Duyvesteyn, H.M.E., Carrique, L., Ren, J., Stuart, D.I., Fry, E.E., Zhao, Y., Malinauskas, T., Zhou, D.

(2020) bioRxiv

DOI: https://doi.org/10.1101/2020.08.13.249177

Macromolecule Content

Total Structure Weight: 442.41 kDa
Atom Count: 26,472
Modelled Residue Count: 3,267
Deposited Residue Count: 3,864
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	1,288	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
Glycosylation
Glycosylation Sites: 17	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	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
STE (Subject of Investigation/LOI) Query on STE 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] mmCIF format, chain EA [auth A] mmCIF format, chain EB [auth C] mmCIF format, chain RA [auth B]	EA [auth A], EB [auth C], RA [auth B]	STEARIC ACID C₁₈ H₃₆ O₂ QIQXTHQIDYTFRH-UHFFFAOYSA-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]
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 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 NA [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 AA [auth A] MOL2 format, chain AB [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 NA [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] 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 CA [auth A] mmCIF format, chain CB [auth C] mmCIF format, chain DA [auth A] mmCIF format, chain DB [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 KA [auth B] mmCIF format, chain LA [auth B] mmCIF format, chain MA [auth B] mmCIF format, chain NA [auth B] mmCIF format, chain OA [auth B] mmCIF format, chain PA [auth B] mmCIF format, chain QA [auth B] 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 V [auth A] 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] mmCIF format, chain ZA [auth C]	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], FA [auth B], GA [auth B], HA [auth B], IA [auth B], JA [auth B], KA [auth B], LA [auth B], MA [auth B], NA [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 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 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 NA [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 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 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 NA [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]