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vg40069 nf  (Sino Biological)


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    Sino Biological vg40069 nf
    Vg40069 Nf, supplied by Sino Biological, used in various techniques. Bioz Stars score: 93/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/vg40069+nf/MERS-CoV+(HCoV-EMC%2F2012)+Spike+Protein+(Codon+Optimized)+Gene+ORF+cDNA+clone+expression+plasmid%2C+N-Flag+tag/pm38428397-222-233-230
    Average 93 stars, based on 3 article reviews
    vg40069 nf - by Bioz Stars, 2026-11
    93/100 stars

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    Article Title: Rapid simulation of glycoprotein structures by grafting and steric exclusion of glycan conformer libraries.
    Article Snippet: Masiulis et al.22 PDB: 6HUO MERS-CoV S structure in complex with 5-N-acetyl neuraminic acid Park et al.90 PDB: 6Q04 Cryo-EM structure of MERS-CoV spike protein, all RBD-down conformation This paper PDB: 7YN0 Cryo-EM structure of MERS-CoV spike protein, intermediate conformation This paper PDB: 7YMZ Cryo-EM structure of MERS-CoV spike protein, One RBD-up conformation 1 This paper PDB: 7YMY Cryo-EM structure of MERS-CoV spike protein, One RBD-up conformation 2 This paper PDB: 7YMX Cryo-EM structure of MERS-CoV spike protein, all RBD-down conformation This paper EMD-33949 Cryo-EM structure of MERS-CoV spike protein, intermediate conformation This paper EMD-33948 Cryo-EM structure of MERS-CoV spike protein, One RBD-up conformation 1 This paper EMD-33947 Cryo-EM structure of MERS-CoV spike protein, One RBD-up conformation 2 This paper EMD-33946 Fourier-cropped cryo-EM map of SARS-CoV-2 S-D614G (corresponding to PDB:7EAZ and EMDB:EMD-31047) This paper EMD-38650 Experimental models: Cell lines Expi293F Cells ThermoFisher Cat# A14527 HEK293 Freestyle ThermoFisher Cat# R79007 Recombinant DNA pcDNA3.1 CD33-N-cadherin (EC1-EC5; residues 160-712) This paper Custom synthesis based on Uniprot ID: NP_031690.3 pcDNA3.1 CD33-N-cadherin (EC4-EC5; residues 331-542) This paper Custom synthesis based on Uniprot ID: NP_031690.3 SARS-CoV-2 S protein with the D614G mutation in pcDNA3.4-TOPO This paper Custom synthesis based on Uniprot ID: P0DTC2 SARS-CoV S protein with the 2P mutation in pcDNA3.4-TOPO This paper Subcloned from Sino Biological Cat# VG40150-G-N (GenBank ID: AAP13567.1) MERS-CoV S protein with the 2P mutation in pcDNA3.4-TOPO This paper Subcloned from Sino Biological Cat# VG40069-NF (GenBank ID: APF29071.1) (Continued on next page) ll OPEN ACCESS Cell 187, 1296–1311.e1–e15, February 29, 2024 e2 Resource

    Mutagenesis:

    Article Title: Rapid simulation of glycoprotein structures by grafting and steric exclusion of glycan conformer libraries.
    Article Snippet: Masiulis et al.22 PDB: 6HUO MERS-CoV S structure in complex with 5-N-acetyl neuraminic acid Park et al.90 PDB: 6Q04 Cryo-EM structure of MERS-CoV spike protein, all RBD-down conformation This paper PDB: 7YN0 Cryo-EM structure of MERS-CoV spike protein, intermediate conformation This paper PDB: 7YMZ Cryo-EM structure of MERS-CoV spike protein, One RBD-up conformation 1 This paper PDB: 7YMY Cryo-EM structure of MERS-CoV spike protein, One RBD-up conformation 2 This paper PDB: 7YMX Cryo-EM structure of MERS-CoV spike protein, all RBD-down conformation This paper EMD-33949 Cryo-EM structure of MERS-CoV spike protein, intermediate conformation This paper EMD-33948 Cryo-EM structure of MERS-CoV spike protein, One RBD-up conformation 1 This paper EMD-33947 Cryo-EM structure of MERS-CoV spike protein, One RBD-up conformation 2 This paper EMD-33946 Fourier-cropped cryo-EM map of SARS-CoV-2 S-D614G (corresponding to PDB:7EAZ and EMDB:EMD-31047) This paper EMD-38650 Experimental models: Cell lines Expi293F Cells ThermoFisher Cat# A14527 HEK293 Freestyle ThermoFisher Cat# R79007 Recombinant DNA pcDNA3.1 CD33-N-cadherin (EC1-EC5; residues 160-712) This paper Custom synthesis based on Uniprot ID: NP_031690.3 pcDNA3.1 CD33-N-cadherin (EC4-EC5; residues 331-542) This paper Custom synthesis based on Uniprot ID: NP_031690.3 SARS-CoV-2 S protein with the D614G mutation in pcDNA3.4-TOPO This paper Custom synthesis based on Uniprot ID: P0DTC2 SARS-CoV S protein with the 2P mutation in pcDNA3.4-TOPO This paper Subcloned from Sino Biological Cat# VG40150-G-N (GenBank ID: AAP13567.1) MERS-CoV S protein with the 2P mutation in pcDNA3.4-TOPO This paper Subcloned from Sino Biological Cat# VG40069-NF (GenBank ID: APF29071.1) (Continued on next page) ll OPEN ACCESS Cell 187, 1296–1311.e1–e15, February 29, 2024 e2 Resource .. REAGENT or RESOURCE SOURCE IDENTIFIER MERS-CoV S protein with the fm2P mutation in pcDNA3.4-TOPO This paper Subcloned from Sino Biological Cat# VG40069-NF (GenBank ID: AFS88936.1) hCoV-NL63 S protein with the 2P mutation in pcDNA3.4-TOPO This paper Subcloned from Sino Biological Cat# VG40604-CF (GenBank ID: APF29071.1) hCoV-229E S protein with the 2P mutation in pcDNA3.4-TOPO This paper Subcloned from Sino Biological Cat# VG40605-CF (GenBank ID: APT69883.1) hCoV-HKU1 S protein with the fm2P mutation in pcDNA3.4-TOPO This paper Subcloned from Sino Biological Cat# VG40606-UT (GenBank ID: Q0ZME7.1) Software and algorithms GlyCONFORMER Grothaus et al.38 https://github.com/IsabellGrothaus/ GlyCONFORMER Relion 3.1 Zivanov et al.91 https://www3.mrc-lmb.cam.ac.uk/ relion//index.php?title=Main_Page CryoSPARC v3.2 Punjani et al.92 https://cryosparc.com/ Phenix 1.19.2-4158 Adams et al.93 http://www.phenix-online.org/ Win Coot 0.9.4.1 Emsley et al.94 https://www2.mrc-lmb.cam.ac.uk/ personal/pemsley/coot/ UCSF-ChimeraX 1.2.5 Pettersen et al.95 https://www.rbvi.ucsf.edu/chimerax/ Byonic v3.9.6 Protein Metrics, USA https://proteinmetrics.com/byos/ Byos v3.11 Protein Metrics, USA https://proteinmetrics.com/byos/ ATSAS-3.0.3-1 Manalastas-Cantos et al.96 https://www.embl-hamburg.de/ biosaxs/software.html SAXS deduction program Shih et al.97 N/A Gromacs 2018.2 or newer Abraham et al.98 www.gromacs.org Gromaps Briones et al.99 https://mptg-cbp.github.io/ gromaps.html MDAnalysis-1.1.1 Gowers et al.100 https://www.mdanalysis.org/ numpy-1.21.1 Harris et al.101 Numpy.org Matplotlib-2.2.3 Hunter102 Matplotlib.org mrcfile-1.4.3 Burnley et al.103 https://mrcfile.readthedocs.io/en/ stable/index.html GlycoSHIELD program suite: GlycoSHIELD, GlycoTRAJ, GlycoSASA, GlycoALPHAFOLD This paper Zenodo: https://zenodo.org/records/ 10668375 GlycoDENSITY This paper www.glycoshield.eu Modeller-10.4 Webb and Sali104 https://salilab.org/modeller/ Other Superdex 200 Increase 10/300 GL Cytiva Cat# 28990944 HiLoad 16/600 Superdex 75 pg Cytiva Cat# 28989333 HisPur Cobalt Resin ThermoFisher Cat# 89966 Superose 6 Increase 10/300 GL Cytiva Cat# 29091596 Carbon film 300 mesh Cu Grids Electron Microscopy Sciences Cat# CF300-Cu-50 Quantifoil R1.2/1.3 300-mesh Cu Grids. .. Ted Pella Cat# 658-300-CU-100 ll OPEN ACCESS Resource

    Software:

    Article Title: Rapid simulation of glycoprotein structures by grafting and steric exclusion of glycan conformer libraries.
    Article Snippet: Masiulis et al.22 PDB: 6HUO MERS-CoV S structure in complex with 5-N-acetyl neuraminic acid Park et al.90 PDB: 6Q04 Cryo-EM structure of MERS-CoV spike protein, all RBD-down conformation This paper PDB: 7YN0 Cryo-EM structure of MERS-CoV spike protein, intermediate conformation This paper PDB: 7YMZ Cryo-EM structure of MERS-CoV spike protein, One RBD-up conformation 1 This paper PDB: 7YMY Cryo-EM structure of MERS-CoV spike protein, One RBD-up conformation 2 This paper PDB: 7YMX Cryo-EM structure of MERS-CoV spike protein, all RBD-down conformation This paper EMD-33949 Cryo-EM structure of MERS-CoV spike protein, intermediate conformation This paper EMD-33948 Cryo-EM structure of MERS-CoV spike protein, One RBD-up conformation 1 This paper EMD-33947 Cryo-EM structure of MERS-CoV spike protein, One RBD-up conformation 2 This paper EMD-33946 Fourier-cropped cryo-EM map of SARS-CoV-2 S-D614G (corresponding to PDB:7EAZ and EMDB:EMD-31047) This paper EMD-38650 Experimental models: Cell lines Expi293F Cells ThermoFisher Cat# A14527 HEK293 Freestyle ThermoFisher Cat# R79007 Recombinant DNA pcDNA3.1 CD33-N-cadherin (EC1-EC5; residues 160-712) This paper Custom synthesis based on Uniprot ID: NP_031690.3 pcDNA3.1 CD33-N-cadherin (EC4-EC5; residues 331-542) This paper Custom synthesis based on Uniprot ID: NP_031690.3 SARS-CoV-2 S protein with the D614G mutation in pcDNA3.4-TOPO This paper Custom synthesis based on Uniprot ID: P0DTC2 SARS-CoV S protein with the 2P mutation in pcDNA3.4-TOPO This paper Subcloned from Sino Biological Cat# VG40150-G-N (GenBank ID: AAP13567.1) MERS-CoV S protein with the 2P mutation in pcDNA3.4-TOPO This paper Subcloned from Sino Biological Cat# VG40069-NF (GenBank ID: APF29071.1) (Continued on next page) ll OPEN ACCESS Cell 187, 1296–1311.e1–e15, February 29, 2024 e2 Resource .. REAGENT or RESOURCE SOURCE IDENTIFIER MERS-CoV S protein with the fm2P mutation in pcDNA3.4-TOPO This paper Subcloned from Sino Biological Cat# VG40069-NF (GenBank ID: AFS88936.1) hCoV-NL63 S protein with the 2P mutation in pcDNA3.4-TOPO This paper Subcloned from Sino Biological Cat# VG40604-CF (GenBank ID: APF29071.1) hCoV-229E S protein with the 2P mutation in pcDNA3.4-TOPO This paper Subcloned from Sino Biological Cat# VG40605-CF (GenBank ID: APT69883.1) hCoV-HKU1 S protein with the fm2P mutation in pcDNA3.4-TOPO This paper Subcloned from Sino Biological Cat# VG40606-UT (GenBank ID: Q0ZME7.1) Software and algorithms GlyCONFORMER Grothaus et al.38 https://github.com/IsabellGrothaus/ GlyCONFORMER Relion 3.1 Zivanov et al.91 https://www3.mrc-lmb.cam.ac.uk/ relion//index.php?title=Main_Page CryoSPARC v3.2 Punjani et al.92 https://cryosparc.com/ Phenix 1.19.2-4158 Adams et al.93 http://www.phenix-online.org/ Win Coot 0.9.4.1 Emsley et al.94 https://www2.mrc-lmb.cam.ac.uk/ personal/pemsley/coot/ UCSF-ChimeraX 1.2.5 Pettersen et al.95 https://www.rbvi.ucsf.edu/chimerax/ Byonic v3.9.6 Protein Metrics, USA https://proteinmetrics.com/byos/ Byos v3.11 Protein Metrics, USA https://proteinmetrics.com/byos/ ATSAS-3.0.3-1 Manalastas-Cantos et al.96 https://www.embl-hamburg.de/ biosaxs/software.html SAXS deduction program Shih et al.97 N/A Gromacs 2018.2 or newer Abraham et al.98 www.gromacs.org Gromaps Briones et al.99 https://mptg-cbp.github.io/ gromaps.html MDAnalysis-1.1.1 Gowers et al.100 https://www.mdanalysis.org/ numpy-1.21.1 Harris et al.101 Numpy.org Matplotlib-2.2.3 Hunter102 Matplotlib.org mrcfile-1.4.3 Burnley et al.103 https://mrcfile.readthedocs.io/en/ stable/index.html GlycoSHIELD program suite: GlycoSHIELD, GlycoTRAJ, GlycoSASA, GlycoALPHAFOLD This paper Zenodo: https://zenodo.org/records/ 10668375 GlycoDENSITY This paper www.glycoshield.eu Modeller-10.4 Webb and Sali104 https://salilab.org/modeller/ Other Superdex 200 Increase 10/300 GL Cytiva Cat# 28990944 HiLoad 16/600 Superdex 75 pg Cytiva Cat# 28989333 HisPur Cobalt Resin ThermoFisher Cat# 89966 Superose 6 Increase 10/300 GL Cytiva Cat# 29091596 Carbon film 300 mesh Cu Grids Electron Microscopy Sciences Cat# CF300-Cu-50 Quantifoil R1.2/1.3 300-mesh Cu Grids. .. Ted Pella Cat# 658-300-CU-100 ll OPEN ACCESS Resource

    Electron Microscopy:

    Article Title: Rapid simulation of glycoprotein structures by grafting and steric exclusion of glycan conformer libraries.
    Article Snippet: Masiulis et al.22 PDB: 6HUO MERS-CoV S structure in complex with 5-N-acetyl neuraminic acid Park et al.90 PDB: 6Q04 Cryo-EM structure of MERS-CoV spike protein, all RBD-down conformation This paper PDB: 7YN0 Cryo-EM structure of MERS-CoV spike protein, intermediate conformation This paper PDB: 7YMZ Cryo-EM structure of MERS-CoV spike protein, One RBD-up conformation 1 This paper PDB: 7YMY Cryo-EM structure of MERS-CoV spike protein, One RBD-up conformation 2 This paper PDB: 7YMX Cryo-EM structure of MERS-CoV spike protein, all RBD-down conformation This paper EMD-33949 Cryo-EM structure of MERS-CoV spike protein, intermediate conformation This paper EMD-33948 Cryo-EM structure of MERS-CoV spike protein, One RBD-up conformation 1 This paper EMD-33947 Cryo-EM structure of MERS-CoV spike protein, One RBD-up conformation 2 This paper EMD-33946 Fourier-cropped cryo-EM map of SARS-CoV-2 S-D614G (corresponding to PDB:7EAZ and EMDB:EMD-31047) This paper EMD-38650 Experimental models: Cell lines Expi293F Cells ThermoFisher Cat# A14527 HEK293 Freestyle ThermoFisher Cat# R79007 Recombinant DNA pcDNA3.1 CD33-N-cadherin (EC1-EC5; residues 160-712) This paper Custom synthesis based on Uniprot ID: NP_031690.3 pcDNA3.1 CD33-N-cadherin (EC4-EC5; residues 331-542) This paper Custom synthesis based on Uniprot ID: NP_031690.3 SARS-CoV-2 S protein with the D614G mutation in pcDNA3.4-TOPO This paper Custom synthesis based on Uniprot ID: P0DTC2 SARS-CoV S protein with the 2P mutation in pcDNA3.4-TOPO This paper Subcloned from Sino Biological Cat# VG40150-G-N (GenBank ID: AAP13567.1) MERS-CoV S protein with the 2P mutation in pcDNA3.4-TOPO This paper Subcloned from Sino Biological Cat# VG40069-NF (GenBank ID: APF29071.1) (Continued on next page) ll OPEN ACCESS Cell 187, 1296–1311.e1–e15, February 29, 2024 e2 Resource .. REAGENT or RESOURCE SOURCE IDENTIFIER MERS-CoV S protein with the fm2P mutation in pcDNA3.4-TOPO This paper Subcloned from Sino Biological Cat# VG40069-NF (GenBank ID: AFS88936.1) hCoV-NL63 S protein with the 2P mutation in pcDNA3.4-TOPO This paper Subcloned from Sino Biological Cat# VG40604-CF (GenBank ID: APF29071.1) hCoV-229E S protein with the 2P mutation in pcDNA3.4-TOPO This paper Subcloned from Sino Biological Cat# VG40605-CF (GenBank ID: APT69883.1) hCoV-HKU1 S protein with the fm2P mutation in pcDNA3.4-TOPO This paper Subcloned from Sino Biological Cat# VG40606-UT (GenBank ID: Q0ZME7.1) Software and algorithms GlyCONFORMER Grothaus et al.38 https://github.com/IsabellGrothaus/ GlyCONFORMER Relion 3.1 Zivanov et al.91 https://www3.mrc-lmb.cam.ac.uk/ relion//index.php?title=Main_Page CryoSPARC v3.2 Punjani et al.92 https://cryosparc.com/ Phenix 1.19.2-4158 Adams et al.93 http://www.phenix-online.org/ Win Coot 0.9.4.1 Emsley et al.94 https://www2.mrc-lmb.cam.ac.uk/ personal/pemsley/coot/ UCSF-ChimeraX 1.2.5 Pettersen et al.95 https://www.rbvi.ucsf.edu/chimerax/ Byonic v3.9.6 Protein Metrics, USA https://proteinmetrics.com/byos/ Byos v3.11 Protein Metrics, USA https://proteinmetrics.com/byos/ ATSAS-3.0.3-1 Manalastas-Cantos et al.96 https://www.embl-hamburg.de/ biosaxs/software.html SAXS deduction program Shih et al.97 N/A Gromacs 2018.2 or newer Abraham et al.98 www.gromacs.org Gromaps Briones et al.99 https://mptg-cbp.github.io/ gromaps.html MDAnalysis-1.1.1 Gowers et al.100 https://www.mdanalysis.org/ numpy-1.21.1 Harris et al.101 Numpy.org Matplotlib-2.2.3 Hunter102 Matplotlib.org mrcfile-1.4.3 Burnley et al.103 https://mrcfile.readthedocs.io/en/ stable/index.html GlycoSHIELD program suite: GlycoSHIELD, GlycoTRAJ, GlycoSASA, GlycoALPHAFOLD This paper Zenodo: https://zenodo.org/records/ 10668375 GlycoDENSITY This paper www.glycoshield.eu Modeller-10.4 Webb and Sali104 https://salilab.org/modeller/ Other Superdex 200 Increase 10/300 GL Cytiva Cat# 28990944 HiLoad 16/600 Superdex 75 pg Cytiva Cat# 28989333 HisPur Cobalt Resin ThermoFisher Cat# 89966 Superose 6 Increase 10/300 GL Cytiva Cat# 29091596 Carbon film 300 mesh Cu Grids Electron Microscopy Sciences Cat# CF300-Cu-50 Quantifoil R1.2/1.3 300-mesh Cu Grids. .. Ted Pella Cat# 658-300-CU-100 ll OPEN ACCESS Resource



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    a ELISA screen for identification of potential SARS-CoV-2 RBD binders. Negative control wells containing expression media, and positive control wells containing VNAR E06 (anti-serum albumin) and rabbit monoclonal CR3022-RB (anti-SARS-CoV-2 Spike) are indicated. b Primary screen for identification of neutralizing VNAR domains. Concentration-dependent neutralization of pseudotyped SARS-CoV-2 (black) or SARS-CoV-1 (red) in HEK293T cells transiently expressing ACE2. Data represents mean ± s.e.m. relative luminescence units (RLUs) from n = 3 independent biological experiments. c Left , rank-ordered IC 50 values for neutralizing VNARs from panel ( b ). VNARs with IC 50 < 10 nM (dashed line) were selected for further characterization. Upper right, depiction of primary sequences of selected VNARs, relative length of complementarity determining regions (CDR1, CDR3) and location of cysteine residues (teal) are shown. d Phylogenetic tree of selected virus taxa, divergent lineages of betacoronaviruses are shown. Glycoproteins encoded by the indicated viruses (*) were used to generate pseudoviruses. e Heatmap summarizing IC 50 values for neutralization of the indicated pseudovirus with the indicated VNAR antibody. Values are derived from experiments described in ( f ). f Secondary validation of selected neutralizing VNAR domains. Concentration-dependent neutralization of viral particles pseudotyped with glycoproteins natively encoded by either SARS-CoV-2 (black), SARS-CoV-1 (red), WIV1-CoV (blue). MERS-CoV (green), or VSV (purple) in Calu-3 cells. Cell viability was also assessed in the presence of increasing concentrations of VNARs (yellow). Data represents mean ± s.e.m. RLU values from n = 3 independent biological experiments. g Concentration-dependent neutralization of replication-competent authentic SARS-CoV-2, strain USA_WA1/2020 in Vero E6 cells. Data represents mean ± s.e.m. RFU values from n = 3 independent biological experiments.

    Journal: Nature Communications

    Article Title: Mechanisms of SARS-CoV-2 neutralization by shark variable new antigen receptors elucidated through X-ray crystallography

    doi: 10.1038/s41467-021-27611-y

    Figure Lengend Snippet: a ELISA screen for identification of potential SARS-CoV-2 RBD binders. Negative control wells containing expression media, and positive control wells containing VNAR E06 (anti-serum albumin) and rabbit monoclonal CR3022-RB (anti-SARS-CoV-2 Spike) are indicated. b Primary screen for identification of neutralizing VNAR domains. Concentration-dependent neutralization of pseudotyped SARS-CoV-2 (black) or SARS-CoV-1 (red) in HEK293T cells transiently expressing ACE2. Data represents mean ± s.e.m. relative luminescence units (RLUs) from n = 3 independent biological experiments. c Left , rank-ordered IC 50 values for neutralizing VNARs from panel ( b ). VNARs with IC 50 < 10 nM (dashed line) were selected for further characterization. Upper right, depiction of primary sequences of selected VNARs, relative length of complementarity determining regions (CDR1, CDR3) and location of cysteine residues (teal) are shown. d Phylogenetic tree of selected virus taxa, divergent lineages of betacoronaviruses are shown. Glycoproteins encoded by the indicated viruses (*) were used to generate pseudoviruses. e Heatmap summarizing IC 50 values for neutralization of the indicated pseudovirus with the indicated VNAR antibody. Values are derived from experiments described in ( f ). f Secondary validation of selected neutralizing VNAR domains. Concentration-dependent neutralization of viral particles pseudotyped with glycoproteins natively encoded by either SARS-CoV-2 (black), SARS-CoV-1 (red), WIV1-CoV (blue). MERS-CoV (green), or VSV (purple) in Calu-3 cells. Cell viability was also assessed in the presence of increasing concentrations of VNARs (yellow). Data represents mean ± s.e.m. RLU values from n = 3 independent biological experiments. g Concentration-dependent neutralization of replication-competent authentic SARS-CoV-2, strain USA_WA1/2020 in Vero E6 cells. Data represents mean ± s.e.m. RFU values from n = 3 independent biological experiments.

    Article Snippet: Plasmids used for generating pseudovirus stocks were sourced as follows: plasmid encoding an Env -defective, luciferase-expressing HIV-1 genome (pNL4-3.luc.R-E − ) , was obtained through the NIH AIDS Reagent Program; plasmids encoding SARS-CoV-1 and SARS-CoV-2 Spike were from Fang Li (Addgene plasmid #145031 and #145032, respectively) ; WIV1-CoV Spike was from Alejandro Balazs (Addgene plasmid #164439) ; MERS-CoV Spike was from Sino Biological (VG40069-NF); and VSV-G was from Bob Weinberg (Addgene plasmid #8454).

    Techniques: Enzyme-linked Immunosorbent Assay, Negative Control, Expressing, Positive Control, Concentration Assay, Neutralization, Derivative Assay

    a Sequence alignment between SARS-CoV-1, SARS-CoV-2, and the MERS RBDs. Residues different from SARS-CoV-2 are highlighted in red and the interaction interface for VNAR-3B4 is marked with a blue box. Bolded letters indicate residues critical for the interaction between the RBD and 3B4 with arrows indicating the residues that form a backbone beta-sheet. The sequence alignment is numbered above according to SARS-CoV-2. b Surface representations of SARS-CoV-1 (pink, above) and MERS (green, below) with variant residues colored red. The ACE2 binding interface is highlighted in purple for SARS-CoV-1 and the DPP4 binding interface in orange for MERS. The homology-modeled interaction interface for 3B4 is colored blue for both structures. c Zoomed in view of the modeled interaction interface between 3B4 (blue) and SARS-CoV-1 (pink, above) and MERS (green, below), with 3B4 colored blue in both pictures. Interacting residues are highlighted as in Fig. , showing the backbone interactions in black dashes and sidechain to backbone or sidechain to sidechain interactions shown as yellow dashes. Insets show the orientation of the zoomed in view. d Overlays of the 3B4 interface from modeled RBDs and their matching RBDs obtained by x-ray crystallography. The panel above shows the modeled SARS-CoV-1 RBD, colored pink, aligned with the crystal structure of SARS-CoV-1 RBD bound to ACE2 (PDB id: 2AJF), colored magenta. The panel below shows the modeled MERS RBD, colored light green, aligned with the crystal structure of MERS RBD bound to DPP4 (PDB id: 4L72), colored dark green.

    Journal: Nature Communications

    Article Title: Mechanisms of SARS-CoV-2 neutralization by shark variable new antigen receptors elucidated through X-ray crystallography

    doi: 10.1038/s41467-021-27611-y

    Figure Lengend Snippet: a Sequence alignment between SARS-CoV-1, SARS-CoV-2, and the MERS RBDs. Residues different from SARS-CoV-2 are highlighted in red and the interaction interface for VNAR-3B4 is marked with a blue box. Bolded letters indicate residues critical for the interaction between the RBD and 3B4 with arrows indicating the residues that form a backbone beta-sheet. The sequence alignment is numbered above according to SARS-CoV-2. b Surface representations of SARS-CoV-1 (pink, above) and MERS (green, below) with variant residues colored red. The ACE2 binding interface is highlighted in purple for SARS-CoV-1 and the DPP4 binding interface in orange for MERS. The homology-modeled interaction interface for 3B4 is colored blue for both structures. c Zoomed in view of the modeled interaction interface between 3B4 (blue) and SARS-CoV-1 (pink, above) and MERS (green, below), with 3B4 colored blue in both pictures. Interacting residues are highlighted as in Fig. , showing the backbone interactions in black dashes and sidechain to backbone or sidechain to sidechain interactions shown as yellow dashes. Insets show the orientation of the zoomed in view. d Overlays of the 3B4 interface from modeled RBDs and their matching RBDs obtained by x-ray crystallography. The panel above shows the modeled SARS-CoV-1 RBD, colored pink, aligned with the crystal structure of SARS-CoV-1 RBD bound to ACE2 (PDB id: 2AJF), colored magenta. The panel below shows the modeled MERS RBD, colored light green, aligned with the crystal structure of MERS RBD bound to DPP4 (PDB id: 4L72), colored dark green.

    Article Snippet: Plasmids used for generating pseudovirus stocks were sourced as follows: plasmid encoding an Env -defective, luciferase-expressing HIV-1 genome (pNL4-3.luc.R-E − ) , was obtained through the NIH AIDS Reagent Program; plasmids encoding SARS-CoV-1 and SARS-CoV-2 Spike were from Fang Li (Addgene plasmid #145031 and #145032, respectively) ; WIV1-CoV Spike was from Alejandro Balazs (Addgene plasmid #164439) ; MERS-CoV Spike was from Sino Biological (VG40069-NF); and VSV-G was from Bob Weinberg (Addgene plasmid #8454).

    Techniques: Sequencing, Variant Assay, Binding Assay