7EDG | pdb_00007edg

Cryo-EM structure of SARS-CoV-2 S-UK variant (B.1.1.7), one RBD-up conformation 2

• PDB DOI: https://doi.org/10.2210/pdb7EDG/pdb
• EM Map EMD-31070: EMDB EMDataResource

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


• Deposited: 2021-03-16 Released: 2021-09-01 
• Deposition Author(s): Yang, T.J., Yu, P.Y., Chang, Y.C., Wu, H.C., Hsu, S.T.D.
• Funding Organization(s): Ministry of Science and Technology (MoST, Taiwan), Academia Sinica (Taiwan)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Effect of SARS-CoV-2 B.1.1.7 mutations on spike protein structure and function.

Yang, T.J., Yu, P.Y., Chang, Y.C., Liang, K.H., Tso, H.C., Ho, M.R., Chen, W.Y., Lin, H.T., Wu, H.C., Hsu, S.D.

(2021) Nat Struct Mol Biol 28: 731-739

• PubMed: 34385690 
• DOI: https://doi.org/10.1038/s41594-021-00652-z
• Primary Citation Related Structures: 
  7EDF, 7EDG, 7EDH, 7EDI, 7EDJ, 7EH5


• PubMed Abstract: 
  

  The B.1.1.7 variant of SARS-CoV-2 first detected in the UK harbors amino-acid substitutions and deletions in the spike protein that potentially enhance host angiotensin conversion enzyme 2 (ACE2) receptor binding and viral immune evasion. Here we report cryo-EM structures of the spike protein of B.1.1.7 in the apo and ACE2-bound forms. The apo form showed one or two receptor-binding domains (RBDs) in the open conformation, without populating the fully closed state. All three RBDs were engaged in ACE2 binding. The B.1.1.7-specific A570D mutation introduces a molecular switch that could modulate the opening and closing of the RBD. The N501Y mutation introduces a π-π interaction that enhances RBD binding to ACE2 and abolishes binding of a potent neutralizing antibody (nAb). Cryo-EM also revealed how a cocktail of two nAbs simultaneously bind to all three RBDs, and demonstrated the potency of the nAb cocktail to neutralize different SARS-CoV-2 pseudovirus strains, including B.1.1.7.

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Organizational Affiliation: 
• Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.
Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan.
Academia Sinica Cryo-EM Center, Academia Sinica, Taipei, Taiwan.
Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan.
Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, Taiwan.
Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan. [e-mail].
Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration, microscopy

Macromolecule Content 

• Total Structure Weight: 444.86 kDa 
• Atom Count: 24,715 
• Modeled Residue Count: 3,023 
• Deposited Residue Count: 3,858 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1,286	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
Glycosylation
Glycosylation Sites: 16		Go to GlyGen: P0DTC2-1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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, DA [auth d], EA [auth e], F, FA [auth f], G, GA [auth g], H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	3		N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	HA [auth A], IA [auth A], JA [auth A], KA [auth A], LA [auth B], MA [auth B], NA [auth B], OA [auth B], PA [auth B], QA [auth B], RA [auth B], SA [auth C], TA [auth C], UA [auth C], VA [auth C], WA [auth C], XA [auth C], YA [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-09-01 
Deposition Author(s): Yang, T.J., Yu, P.Y., Chang, Y.C., Wu, H.C., Hsu, S.T.D.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	109-3114-Y-001-001
Academia Sinica (Taiwan)	Taiwan	AS-CDA-109-L08
Academia Sinica (Taiwan)	Taiwan	AS-CFII-108-110
Academia Sinica (Taiwan)	Taiwan	AS-CFII108-111

Revision History  

• Version 1.0: 2021-09-01
  Type: Initial release
  
• Version 1.1: 2022-01-05
  Changes: Database references
• Version 1.2: 2024-10-23
  Changes: Data collection, Structure summary
• Version 1.3: 2025-06-18
  Changes: Data collection