7KJ2

SARS-CoV-2 Spike Glycoprotein with one ACE2 Bound

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

A trimeric human angiotensin-converting enzyme 2 as an anti-SARS-CoV-2 agent.

Xiao, T., Lu, J., Zhang, J., Johnson, R.I., McKay, L.G.A., Storm, N., Lavine, C.L., Peng, H., Cai, Y., Rits-Volloch, S., Lu, S., Quinlan, B.D., Farzan, M., Seaman, M.S., Griffiths, A., Chen, B.

(2021) Nat Struct Mol Biol 28: 202-209

  • DOI: 10.1038/s41594-020-00549-3
  • Primary Citation of Related Structures:  
    7KJ4, 7KJ5, 7KJ2, 7KJ3

  • PubMed Abstract: 

    • Effective intervention strategies are urgently needed to control the COVID-19 pandemic. Human angiotensin-converting enzyme 2 (ACE2) is a membrane-bound carboxypeptidase that forms a dimer and serves as the cellular receptor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ...

    Effective intervention strategies are urgently needed to control the COVID-19 pandemic. Human angiotensin-converting enzyme 2 (ACE2) is a membrane-bound carboxypeptidase that forms a dimer and serves as the cellular receptor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). ACE2 is also a key negative regulator of the renin-angiotensin system that modulates vascular functions. We report here the properties of a trimeric ACE2 ectodomain variant, engineered using a structure-based approach. The trimeric ACE2 variant has a binding affinity of ~60 pM for the spike protein of SARS‑CoV‑2 (compared with 77 nM for monomeric ACE2 and 12-22 nM for dimeric ACE2 constructs), and its peptidase activity and the ability to block activation of angiotensin II receptor type 1 in the renin-angiotensin system are preserved. Moreover, the engineered ACE2 potently inhibits SARS‑CoV‑2 infection in cell culture. These results suggest that engineered, trimeric ACE2 may be a promising anti-SARS-CoV-2 agent for treating COVID-19.

    Related Citations: 
    • A trimeric human angiotensin-converting enzyme 2 as an anti-SARS-CoV-2 agent in vitro.
      Xiao, T., Lu, J., Zhang, J., Johnson, R.I., McKay, L.G.A., Storm, N., Lavine, C.L., Peng, H., Cai, Y., Rits-Volloch, S., Lu, S., Quinlan, B.D., Farzan, M., Seaman, M.S., Griffiths, A., Chen, B.
      (2020) Biorxiv --: --
    Organizational Affiliation: 

    Department of Pediatrics, Harvard Medical School, Boston, MA, USA. bchen@crystal.harvard.edu.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Spike glycoproteinA, B, C1234Severe acute respiratory syndrome coronavirus 2Mutation(s): 2 
Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Angiotensin-converting enzyme 2D615Homo sapiensMutation(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
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, F, G, H, I, J, K, L
E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U
2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG
Download Ideal Coordinates CCD File 
AA [auth A] , AB [auth C] , BA [auth A] , BB [auth C] , CA [auth A] , CB [auth C] , DA [auth A] , DB [auth C] , 
AA [auth A],  AB [auth C],  BA [auth A],  BB [auth C],  CA [auth A],  CB [auth C],  DA [auth A],  DB [auth C],  EA [auth A],  EB [auth D],  FA [auth B],  GA [auth B],  HA [auth B],  IA [auth B],  JA [auth B],  KA [auth B],  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],  V [auth A],  VA [auth C],  W [auth A],  WA [auth C],  X [auth A],  XA [auth C],  Y [auth A],  YA [auth C],  Z [auth A],  ZA [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI147884
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI147884 01A1S1
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI141002
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI127193

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-11
    Type: Initial release
  • Version 1.1: 2021-01-27
    Changes: Database references
  • Version 1.2: 2021-02-24
    Changes: Database references