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National Institute of Allergy and Infectious Disease
NIH 3D
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NIH3D

SARS-CoV-2 Spike S Protein and ACE2 (PathogenAR)

Created by
kbrowne
Created:
9/9/20
Submitted:
10/8/26
Published:
10/8/26
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3DPX-014823

Licensing:

CC-BY
How to cite this NIH 3D entry
612
60
Version 5

Category

Biomacromolecules
Biomacromolecules

Collection(s)

Pathogen AR
Pathogen AR
Description

This model includes SARS-CoV-2 Spike S Protein (open state) and ACE2 (PathogenAR).

This model was not originally intended for 3D Printing, so try at your own risk.

The S protein model was imported from CHARMM-GUI http://www.charmm-gui.org/?doc=archive&lib=covid19 representing open (PDB 6VSB_1_1_1) state into ChimeraX.

With reference to https://pubs.acs.org/doi/10.1021/acs.jpcb.0c0455,  the S1 and S2 domains were colored (amino acids (aa) 1-685, 686-1273), then  predicted regions were colored (amino acids (aa) 1-25, 67-75, 143-155, 177-186, 247-260, 329-334, 455-490, 621-639, 673-686, 829-852, 1148-1273).

The computed lipid membrane was added to the ChimeraX scene from the http://www.charmm-gui.org/?doc=archive&lib=covid1 CHARMM-GUI(6VSB_1_1_1.tgz) and aligned to the above models using the 6VSB model within that file.

ACE2 was added to the scene using data from PDB 6M17 which includes the S protein receptor-binding domain (RBD) and B0AT protein.  B0AT was removed and the RBD was used to align ACE2 to the open RBD in the 6VSB model.

 

Source Data Details