Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy, gel filtration

Macromolecule Content

• Total Structure Weight: 433.91 kDa 
• Atom Count: 23561 
• Modelled Residue Count: 2980 
• Deposited Residue Count: 3855 
• Unique protein chains: 1

7LWV

UK (B.1.1.7) SARS-CoV-2 spike protein variant (S-GSAS-B.1.1.7) in the 1-RBD-up conformation

• PDB DOI: 10.2210/pdb7LWV/pdb
• EM Map EMD-23558:EMDBEMDataResource

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


• Deposited: 2021-03-01 Released: 2021-03-31 
• Deposition Author(s): Gobeil, S., Acharya, P.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.12 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Effect of natural mutations of SARS-CoV-2 on spike structure, conformation, and antigenicity.

Gobeil, S.M., Janowska, K., McDowell, S., Mansouri, K., Parks, R., Stalls, V., Kopp, M.F., Manne, K., Li, D., Wiehe, K., Saunders, K.O., Edwards, R.J., Korber, B., Haynes, B.F., Henderson, R., Acharya, P.

(2021) Science 373

• PubMed: 34168071 
• DOI: 10.1126/science.abi6226
• Primary Citation of Related Structures:  
  7LWI, 7LWJ, 7LWK, 7LWL, 7LWM, 7LWN, 7LWO, 7LWP, 7LWQ, 7LWT, 7LWU, 7LWV, 7LWW, 7LYM


• PubMed Abstract: 
  

SARS-CoV-2 variants with multiple spike mutations enable increased transmission and antibody resistance. Here, we combine cryo-EM, binding and computational analyses to study variant spikes, including one that was involved in transmission between minks and humans, and others that originated and spread in human populations. All variants showed increased ACE2 receptor binding and increased propensity for RBD up states. While adaptation to mink resulted in spike destabilization, the B.1.1.7 (UK) spike balanced stabilizing and destabilizing mutations. A local destabilizing effect of the RBD E484K mutation was implicated in resistance of the B.1.1.28/P.1 (Brazil) and B.1.351 (South Africa) variants to neutralizing antibodies. Our studies revealed allosteric effects of mutations and mechanistic differences that drive either inter-species transmission or escape from antibody neutralization.

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Related Citations: 

• Effect of natural mutations of SARS-CoV-2 on spike structure, conformation and antigenicity.
  Gobeil, S.M., Janowska, K., McDowell, S., Mansouri, K., Parks, R., Stalls, V., Kopp, M.F., Manne, K., Saunders, K., Edwards, R.J., Haynes, B.F., Henderson, R.C., Acharya, P.
  (2021) Biorxiv --: --

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Organizational Affiliation: 

Department of Biochemistry, Duke University, Durham, NC 27710, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1285	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 10  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	AA [auth C], BA [auth C], CA [auth C], D [auth A], DA [auth C], E [auth A], EA [auth C], F [auth A], FA [auth C], G [auth A], GA [auth C], H [auth A], HA [auth C], I [auth A], IA [auth C], J [auth A], JA [auth C], K [auth A], KA [auth C], L [auth A], M [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth C], Z [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: 3.12 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2021-03-01 
• Released Date: 2021-03-31 
Deposition Author(s): Gobeil, S., Acharya, P.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI145687

Revision History  

• Version 1.0: 2021-03-31
  Type: Initial release
  
• Version 1.1: 2021-04-07
  Changes: Database references
• Version 2.0: 2021-06-30
  Type: Coordinate replacement
  Reason: Polymer geometry
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Refinement description
• Version 2.1: 2021-07-07
  Changes: Database references
• Version 2.2: 2021-08-18
  Changes: Database references