|Entry||Database: PDB / ID: 7lyk|
|Title||South African (B.1.351) SARS-CoV-2 spike protein variant (S-GSAS-B.1.351) in the 2-RBD-up conformation|
|Keywords||VIRAL PROTEIN / SARS-CoV-2 Spike Protein Trimer|
|Function / homology|
Function and homology information
suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / endoplasmic reticulum-Golgi intermediate compartment / viral translation / host cell surface receptor binding / endocytosis involved in viral entry into host cell / endocytic vesicle membrane / viral protein processing / fusion of virus membrane with host plasma membrane ...suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / endoplasmic reticulum-Golgi intermediate compartment / viral translation / host cell surface receptor binding / endocytosis involved in viral entry into host cell / endocytic vesicle membrane / viral protein processing / fusion of virus membrane with host plasma membrane / suppression by virus of host type I interferon-mediated signaling pathway / fusion of virus membrane with host endosome membrane / viral envelope / viral entry into host cell / go:0009405: / endoplasmic reticulum lumen / host cell plasma membrane / virion membrane / integral component of membrane / identical protein binding
Spike receptor binding domain superfamily, coronavirus / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Spike glycoprotein S2 superfamily, coronavirus / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike glycoprotein S2, coronavirus / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / in:ipr027400: / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like
|Biological species||Severe acute respiratory syndrome coronavirus 2|
|Method||ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.65 Å|
|Authors||Gobeil, S. / Acharya, P.|
|Funding support|| United States, 1items |
|Citation||Journal: bioRxiv / Year: 2021|
Title: Effect of natural mutations of SARS-CoV-2 on spike structure, conformation and antigenicity.
Authors: Sophie M-C Gobeil / Katarzyna Janowska / Shana McDowell / Katayoun Mansouri / Robert Parks / Victoria Stalls / Megan F Kopp / Kartik Manne / Kevin Saunders / Robert J Edwards / Barton F ...Authors: Sophie M-C Gobeil / Katarzyna Janowska / Shana McDowell / Katayoun Mansouri / Robert Parks / Victoria Stalls / Megan F Kopp / Kartik Manne / Kevin Saunders / Robert J Edwards / Barton F Haynes / Rory C Henderson / Priyamvada Acharya
Abstract: New SARS-CoV-2 variants that have accumulated multiple mutations in the spike (S) glycoprotein enable increased transmission and resistance to neutralizing antibodies. Here, we study the antigenic ...New SARS-CoV-2 variants that have accumulated multiple mutations in the spike (S) glycoprotein enable increased transmission and resistance to neutralizing antibodies. Here, we study the antigenic and structural impacts of the S protein mutations from four variants, one that was involved in transmission between minks and humans, and three that rapidly spread in human populations and originated in the United Kingdom, Brazil or South Africa. All variants either retained or improved binding to the ACE2 receptor. The B.1.1.7 (UK) and B.1.1.28 (Brazil) spike variants showed reduced binding to neutralizing NTD and RBD antibodies, respectively, while the B.1.351 (SA) variant showed reduced binding to both NTD- and RBD-directed antibodies. Cryo-EM structural analyses revealed allosteric effects of the mutations on spike conformations and revealed mechanistic differences that either drive inter-species transmission or promotes viral escape from dominant neutralizing epitopes.
Highlights: Cryo-EM structures reveal changes in SARS-CoV-2 S protein during inter-species transmission or immune evasion.Adaptation to mink resulted in increased ACE2 binding and spike ...Highlights: Cryo-EM structures reveal changes in SARS-CoV-2 S protein during inter-species transmission or immune evasion.Adaptation to mink resulted in increased ACE2 binding and spike destabilization.B.1.1.7 S mutations reveal an intricate balance of stabilizing and destabilizing effects that impact receptor and antibody binding.E484K mutation in B.1.351 and B.1.1.28 S proteins drives immune evasion by altering RBD conformation.S protein uses different mechanisms to converge upon similar solutions for altering RBD up/down positioning.
SummaryFull reportAbout validation report
|Structure viewer||Molecule: |
Downloads & links
A: Spike glycoprotein
B: Spike glycoprotein
C: Spike glycoprotein
Mass: 142325.469 Da / Num. of mol.: 3
Mutation: N501Y, K417N, E484K, L18F, D80A, D215G, R246I, A701V, D614G, R682G, R683S, R685S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Variant: South African (B.1.351) / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C8H15NO6
|Has ligand of interest||N|
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction|
|Component||Name: South African (B.1.351) SARS-CoV-2 spike protein variant (S-GSAS-B.1.351)|
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
|Source (natural)||Organism: Severe acute respiratory syndrome coronavirus 2|
|Source (recombinant)||Organism: Homo sapiens (human)|
|Buffer solution||pH: 8|
|Specimen||Conc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Vitrification||Cryogen name: ETHANE|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Microscopy||Model: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER|
|Electron lens||Mode: BRIGHT FIELDBright-field microscopy|
|Image recording||Electron dose: 51.16 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|3D reconstruction||Resolution: 3.65 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 200301 / Symmetry type: POINT|
|Atomic model building||Protocol: AB INITIO MODEL|
|Atomic model building|
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