Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 385.30 kDa 
• Atom Count: 24052 
• Modelled Residue Count: 3058 
• Deposited Residue Count: 3381 
• Unique protein chains: 1

7CN9

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

• DOI: 10.2210/pdb7CN9/pdb
• EMDataResource: EMD-30419

• 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.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

A Carbohydrate-Binding Protein from the Edible Lablab Beans Effectively Blocks the Infections of Influenza Viruses and SARS-CoV-2.

Liu, Y.M., Shahed-Al-Mahmud, M., Chen, X., Chen, T.H., Liao, K.S., Lo, J.M., Wu, Y.M., Ho, M.C., Wu, C.Y., Wong, C.H., Jan, J.T., Ma, C.

(2020) Cell Rep 32: 108016-108016

• PubMed: 32755598 
• DOI: 10.1016/j.celrep.2020.108016
• Primary Citation of Related Structures:  
  7CN9


• PubMed Abstract: 
  

The influenza virus hemagglutinin (HA) and coronavirus spike (S) protein mediate virus entry. HA and S proteins are heavily glycosylated, making them potential targets for carbohydrate binding agents such as lectins. Here, we show that the lectin FRIL, isolated from hyacinth beans (Lablab purpureus), has anti-influenza and anti-SARS-CoV-2 activity. FRIL can neutralize 11 representative human and avian influenza strains at low nanomolar concentrations, and intranasal administration of FRIL is protective against lethal H1N1 infection in mice. FRIL binds preferentially to complex-type N-glycans and neutralizes viruses that possess complex-type N-glycans on their envelopes. As a homotetramer, FRIL is capable of aggregating influenza particles through multivalent binding and trapping influenza virions in cytoplasmic late endosomes, preventing their nuclear entry. Remarkably, FRIL also effectively neutralizes SARS-CoV-2, preventing viral protein production and cytopathic effect in host cells. These findings suggest a potential application of FRIL for the prevention and/or treatment of influenza and COVID-19.

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Organizational Affiliation: 

Genomics Research Center, Academia Sinica, Taipei 115, Taiwan. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1127	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

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
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], K [auth f], M [auth H], N	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
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
Glycosylation Resources
GlyTouCan:  G21290RB GlyCosmos:  G21290RB GlyGen:  G21290RB

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
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
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
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
Glycosylation Resources
GlyTouCan:  G22573RC GlyCosmos:  G22573RC GlyGen:  G22573RC

Entity ID: 6
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
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
Glycosylation Resources
GlyTouCan:  G81315DD GlyCosmos:  G81315DD GlyGen:  G81315DD

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2020-07-30 
• Released Date: 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.

Revision History  

• Version 1.0: 2020-08-26
  Type: Initial release
  
• Version 1.1: 2021-03-10
  Changes: Structure summary