Biological Assembly 1  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A3B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 507.72 kDa 
• Atom Count: 30463 
• Modelled Residue Count: 3825 
• Deposited Residue Count: 4515 
• Unique protein chains: 2

7A94

SARS-CoV-2 Spike Glycoprotein with 1 ACE2 Bound

• PDB DOI: 10.2210/pdb7A94/pdb
• EM Map EMD-11684:EMDBEMDataResource

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


• Deposited: 2020-09-01 Released: 2020-09-16 
• Deposition Author(s): Benton, D.J., Wrobel, A.G., Rosenthal, P.B., Gamblin, S.J.
• Funding Organization(s): The Francis Crick Institute

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Receptor binding and priming of the spike protein of SARS-CoV-2 for membrane fusion.

Benton, D.J., Wrobel, A.G., Xu, P., Roustan, C., Martin, S.R., Rosenthal, P.B., Skehel, J.J., Gamblin, S.J.

(2020) Nature 588: 327-330

• PubMed: 32942285 
• DOI: 10.1038/s41586-020-2772-0
• Primary Citation of Related Structures:  
  7A91, 7A92, 7A93, 7A94, 7A95, 7A96, 7A97, 7A98


• PubMed Abstract: 
  

Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is initiated by virus binding to the ACE2 cell-surface receptors ^1-4 , followed by fusion of the virus and cell membranes to release the virus genome into the cell. Both receptor binding and membrane fusion activities are mediated by the virus spike glycoprotein ^5-7 . As with other class-I membrane-fusion proteins, the spike protein is post-translationally cleaved, in this case by furin, into the S1 and S2 components that remain associated after cleavage ^8-10 . Fusion activation after receptor binding is proposed to involve the exposure of a second proteolytic site (S2'), cleavage of which is required for the release of the fusion peptide ^11,12 . Here we analyse the binding of ACE2 to the furin-cleaved form of the SARS-CoV-2 spike protein using cryo-electron microscopy. We classify ten different molecular species, including the unbound, closed spike trimer, the fully open ACE2-bound trimer and dissociated monomeric S1 bound to ACE2. The ten structures describe ACE2-binding events that destabilize the spike trimer, progressively opening up, and out, the individual S1 components. The opening process reduces S1 contacts and unshields the trimeric S2 core, priming the protein for fusion activation and dissociation of ACE2-bound S1 monomers. The structures also reveal refolding of an S1 subdomain after ACE2 binding that disrupts interactions with S2, which involves Asp614 ^13-15 and leads to the destabilization of the structure of S2 proximal to the secondary (S2') cleavage site.

---

Organizational Affiliation: 

Strutural Biology of Disease Processes Laboratory, Francis Crick Institute, London, UK. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1287	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 2  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Angiotensin-converting enzyme 2	D	654	Homo sapiens	Mutation(s): 0  Gene Names: ACE2, UNQ868/PRO1885 EC: 3.4.17.23 (PDB Primary Data), 3.4.17 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYF1 (Homo sapiens) Explore Q9BYF1  Go to UniProtKB:  Q9BYF1
PHAROS:  Q9BYF1 GTEx:  ENSG00000130234

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	AA [auth C], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], 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 C], U [auth C], V [auth C], W [auth C], X [auth C], Y [auth C], Z [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN	BA [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2020-09-01 
• Released Date: 2020-09-16 
Deposition Author(s): Benton, D.J., Wrobel, A.G., Rosenthal, P.B., Gamblin, S.J.

---

Funding Organization	Location	Grant Number
The Francis Crick Institute	United Kingdom	FC001078
The Francis Crick Institute	United Kingdom	FC001143

Revision History  

• Version 1.0: 2020-09-16
  Type: Initial release
  
• Version 1.1: 2020-09-23
  Changes: Database references
• Version 1.2: 2020-09-30
  Changes: Database references
• Version 1.3: 2020-12-16
  Changes: Database references