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NIH3D

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

Created by
kbrowne
Created:
9/9/20
Submitted:
3/6/23
Published:
3/6/23

Select an image below to view

3DPX-014823

Licensing:

CC-BY
268
37
Version 2

Category

Biomacromolecules
Biomacromolecules

Collection(s)

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.

The FBX file included is the version created for the app and is UV mapped.  Textures are included with image files.

Other formats were created for the 3DPX viewer, but may be useful in other applications.

 

SProtein_ACE2-AO.jpg
SProtein_HostMembrane-TM_u0_v0.tif_Comp.jpg
SProteinViral_Membrane-TMAOCa20.jpg
SProtein_HostMembrane-AO_u0_v0.jpg
SProtein_HostMembrane-TM_u0_v0.jpg
SProtein_ACE2-TM_u0_v0.jpg
SProtein_Spike_01-TM_u0_v0_1.jpg
SProteinViral_Membrane-AO_u0_v0.jpg
SProtein_Spike_01-AO_u0_v0_1.jpg
SpikeAce_Render.jpg