7CN9

Cryo-EM structure of SARS-CoV-2 Spike ectodomain

PDB DOI: https://doi.org/10.2210/pdb7CN9/pdb
EM Map EMD-30419: EMDB EMDataResource

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

Deposited: 2020-07-30 Released: 2020-08-26
Deposition Author(s): Ho, M., Chang, Y., Wang, C., Wu, Y., Huang, H., Chen, T., Lo, J.M., Chen, X., Ma, C.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.70 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.

Macromolecule Content

Total Structure Weight: 385.3 kDa
Atom Count: 24,052
Modelled Residue Count: 3,058
Deposited Residue Count: 3,381
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	1,127	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 5 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

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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 [auth E], E [auth X], H [auth W], I [auth Z], J [auth d], D [auth E], E [auth X], H [auth W], I [auth Z], J [auth d], K [auth f], M [auth H], N	2		N-Glycosylation	Interactions Focus chain D [auth E] Focus chain E [auth X] Focus chain H [auth W] Focus chain I [auth Z] Focus chain J [auth d] Focus chain K [auth f] Focus chain M [auth H] Focus chain N Interactions & Density Focus chain D [auth E] Focus chain E [auth X] Focus chain H [auth W] Focus chain I [auth Z] Focus chain J [auth d] Focus chain K [auth f] Focus chain M [auth H] Focus chain N
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	F [auth k]	3		N-Glycosylation	Interactions Focus chain F [auth k] Interactions & Density Focus chain F [auth k]
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G [auth p], P [auth V]	3		N-Glycosylation	Interactions Focus chain G [auth p] Focus chain P [auth V] Interactions & Density Focus chain G [auth p] Focus chain P [auth V]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	L [auth h]	4		N-Glycosylation	Interactions Focus chain L [auth h] Interactions & Density Focus chain L [auth h]
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Entity ID: 6
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	O [auth Q]	4		N-Glycosylation	Interactions Focus chain O [auth Q] Interactions & Density Focus chain O [auth Q]
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

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 AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain HA [auth C] SDF format, chain IA [auth C] SDF format, chain JA [auth C] SDF format, chain KA [auth C] SDF format, chain LA [auth C] SDF format, chain MA [auth C] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain Z [auth B] SDF format, chain GA [auth C] SDF format, chain X [auth B] SDF format, chain Y [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain KA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain MA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain Z [auth B] MOL2 format, chain GA [auth C] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] EA [auth B] AA [auth B], BA [auth B], CA [auth B], DA [auth B], EA [auth B], FA [auth B], GA [auth C], HA [auth C], IA [auth C], JA [auth C], KA [auth C], LA [auth C], MA [auth C], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth B], Y [auth B], Z [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]