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"SARS (2002) Spike S-2P with Receptor Binding Domain (RBD) down in the inactive conformation"

Submitted by:

cruzp2
Tue, 2020-01-28 12:06

✓ This model was processed by NetFabb
Model ID
3DPX-012877
Category
Proteins, Macromolecules and Viruses
Keyword(s)
virus, SARS, Spike, surface, stabilized

SARS (2002) spike protein S-2P with RBD down in the inactive conformation. This has been stabilized in the prefusion conformation with two proline mutations. One protomer has its domains colored as follows:

Blue: N-Terminal Domain (NTD)

Green: Receptor Binding Domain (RBD)

Tan: Remainder of S1

Red: Remainder of S2

See also 3dpx-014102 for a related structure from SARS-CoV-2 with one RBD up in the active conformation.
Model Origin
Molecular data (e.g., crystallography)

Digital Object Identifier (DOI)
10.1038/s41598-018-34171-7
Author(s)
Kirchdoerfer RN, Wang N, Pallesen J, Wrapp D, Turner HL, Cottrell CA, Corbett KS, Graham BS, McLellan JS, Ward AB
Citation Title
Stabilized coronavirus spikes are resistant to conformational changes induced by receptor recognition or proteolysis
Journal
Scientific Reports
Citation Year
2018
Volume
8
Issue
1
Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV) emerged in 2002 as a highly transmissible pathogenic human betacoronavirus. The viral spike glycoprotein (S) utilizes angiotensin-converting enzyme 2 (ACE2) as a host protein receptor and mediates fusion of the viral and host membranes, making S essential to viral entry into host cells and host species tropism. As SARS-CoV enters host cells, the viral S is believed to undergo a number of conformational transitions as it is cleaved by host proteases and binds to host receptors. We recently developed stabilizing mutations for coronavirus spikes that prevent the transition from the pre-fusion to post-fusion states. Here, we present cryo-EM analyses of a stabilized trimeric SARS-CoV S, as well as the trypsin-cleaved, stabilized S, and its interactions with ACE2. Neither binding to ACE2 nor cleavage by trypsin at the S1/S2 cleavage site impart large conformational changes within stabilized SARS-CoV S or expose the secondary cleavage site, S2′.

multiple files read like this..[Wuhan CoV surface.wrl]

See for yourself https://3dprint.nih.gov/discover/3dpx-012877

Heres another for you

"SARS-CoV-2 spike protein 6VSB with one Receptor Binding Domain (RBD) up in the active conformation"

✓ This model was processed by NetFabb
Model ID
3DPX-014102
Category
Proteins, Macromolecules and Viruses
Keyword(s)
SARS-CoV-2, COVID-19, coronavirus spike glycoprotein
Protein Data Bank ID
6VSB

SARS-CoV-2 spike protein from 6VSB. The protomer that has its Receptor Binding Domain (RBD) flipped into the up (active) conformation has its domains colored as described in Figure 1 of: Wrapp, D., Wang, N., Corbett, K.S., Goldsmith, J.A., Hsieh, C.L., Abiona, O., Graham, B.S., McLellan, J.S. (2020) Science 367: 1260-1263

Blue: N-Terminal Domain (NTD)

Green: Receptor Binding Domain (RBD)

Tan: Remainder of S1

Cyan: Fusion Peptide

Yellow: Heptad Repeat 1

Orange: Central Helix

Purple: Connector Domain

Red: Remainder of S2

See also 3dpx-012877 for a related structure from SARS-CoV with all RBD down in the inactive conformation.