Virus:Article Title: Cryo-EM Structures of Eastern Equine Encephalitis Virus Reveal Mechanisms of Virus Disassembly and Antibody Neutralization
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies EEEV-3 Diamond Lab Kim et al., 2018 EEEV-5 Diamond Lab Kim et al., 2018 EEEV-42 Diamond Lab Kim et al., 2018 EEEV-58 Diamond Lab Kim et al., 2018 EEEV-69 Diamond Lab Kim et al., 2018 H77.39 Diamond Lab Sabo et al., 2011 Peroxidase AffiniPure Goat Anti-Mouse IgG (H+L) Jackson ImmunoResearch 115-032-062 Bacterial and Virus Strains SINV(TR339)-EEEV(FL93-939) chimera Kim et al., 2018 N/A SINV-TR339 Klimstra et al., 2003 N/A Chemicals, Peptides, and Recombinant Proteins Acetonitrile Fisher Scientific Cat# 10489553 Procainamide hydrochloride Abcam Cat# ab120955 Dithiothreitol Sigma-Aldrich Cat# 43819 Ammonium formate buffer Waters Cat# 186007081 Sodium cyanoborohydride Sigma-Aldrich Cat# 156159 DMSO Sigma-Aldrich Cat# D2438 Acetic acid Fisher Scientific Cat# 10384970 PNGase F New England BioLabs Cat# P0705S Endoglycosidase H New England BioLabs Cat# P0702S PNGase A New England BioLabs Cat# P0707S Critical Commercial Assays Pierce Fab Preparation Kit Thermo Scientific Cat# 44985 Deposited Data CryoEM map of native SINV-EEEV chimera (4.4Å) This paper EMD-9280 CryoEM map of native SINV-EEEV chimera showing N-terminal chain (4.8Å) This paper EMD-9281 CryoEM map of SINV-EEEV chimera with Fab of EEEV-3 This paper EMD-9274 CryoEM map of SINV-EEEV chimera with Fab of EEEV-5 This paper EMD-9275 CryoEM map of SINV-EEEV chimera with Fab of EEEV-42 This paper EMD-9249 CryoEM map of SINV-EEEV chimera with Fab of EEEV-58 This paper EMD-9278 CryoEM map of SINV-EEEV chimera with Fab of EEEV-69 This paper EMD-9279 Coordinates of E1-E2-capsid protein for native SINV-EEEV cryoEM map This paper PDB ID 6MX4 Coordinates of capsid protein for native SINV-EEEV cryoEM map This paper PDB ID 6MX7 Coordinates of E1-E2 ecto-domains and fitted Fab homolog in SINV-EEEV: EEEV-3 cryoEM map This paper PDB ID 6MW9 Coordinates of E1-E2 ecto-domains and fitted Fab homolog in SINV-EEEV: EEEV-5 cryoEM map This paper PDB ID 6MWC Coordinates of E1-E2 ecto-domains and fitted Fab homolog in SINV-EEEV: EEEV-42 cryoEM map This paper PDB ID 6MUI Coordinates of E1-E2 ecto-domains and fitted Fab homolog in SINV-EEEV: EEEV-58 cryoEM map This paper PDB ID 6MWV Coordinates of E1-E2 ecto-domains and fitted Fab homolog in SINV-EEEV: EEEV-69 cryoEM map This paper PDB ID 6MWX (Continued on next page) e1 Cell Reports 25, 3136–3147.e1–e5, December 11, 2018 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental Models: Cell Lines African green monkey kidney (Vero) cell WHO Reference Cell Bank WHO Vero cells Baby Hamster Kidney (BHK)-15 cells Kuhn Lab (Purdue University) N/A Aedes albopictus C6/36 ATCC Cat#CRL-1660 Raji B cells expressing DC-SIGN Kwon et al., 2002 N/A Raji B cells expressing L-SIGN Kwon et al., 2002 N/A Raji B cells Kwon et al., 2002 N/A Software and Algorithms Prism GraphPad Software Prism Version 7.0d Empower 3.0 Waters N/A NetNGlyc 1.0 http://www.cbs.dtu.dk/ services/NetNGlyc/ N/A Leginon Carragher et al., 2000 N/A Motioncor2 Zheng et al., 2017 N/A CTFFIND4 Rohou and Grigorieff, 2015 N/A Appion Lander et al., 2009 N/A Relion Scheres, 2012 N/A jspr Guo and Jiang, 2014 N/A ResMap Kucukelbir et al., 2014 N/A Phenix Real Space Refine Adams et al., 2010 N/A Rosetta Alford et al., 2017 N/A MolProbity Chen et al., 2010 N/A COOT Emsley and Cowtan, 2004 N/A PyMol https://pymol.org/2/ N/A Chimera Pettersen et al., 2004 N/A RIVEM Xiao and Rossmann, 2007 N/A EMfit Rossmann et al., 2001 N/A I-TASSER Yang et al., 2015 N/A Clustal Omega Sievers et al., 2011 N/A ESpript Gouet et al., 2003 N/A ExPasy Gasteiger et al., 2003 N/A Other Spe-ed Amide 2 cartridges Applied Separations Cat# 4821 Glycan BEH Amide column (2.1 mm x 100 mm, 1.7 mM) Waters Cat# 186004741 PVDF protein-binding membrane Millipore Cat# MAIPS4510 Ultrathin continuous carbon grids Ted Pella Cat# 01824
Recombinant:Article Title: Cryo-EM Structures of Eastern Equine Encephalitis Virus Reveal Mechanisms of Virus Disassembly and Antibody Neutralization
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies EEEV-3 Diamond Lab Kim et al., 2018 EEEV-5 Diamond Lab Kim et al., 2018 EEEV-42 Diamond Lab Kim et al., 2018 EEEV-58 Diamond Lab Kim et al., 2018 EEEV-69 Diamond Lab Kim et al., 2018 H77.39 Diamond Lab Sabo et al., 2011 Peroxidase AffiniPure Goat Anti-Mouse IgG (H+L) Jackson ImmunoResearch 115-032-062 Bacterial and Virus Strains SINV(TR339)-EEEV(FL93-939) chimera Kim et al., 2018 N/A SINV-TR339 Klimstra et al., 2003 N/A Chemicals, Peptides, and Recombinant Proteins Acetonitrile Fisher Scientific Cat# 10489553 Procainamide hydrochloride Abcam Cat# ab120955 Dithiothreitol Sigma-Aldrich Cat# 43819 Ammonium formate buffer Waters Cat# 186007081 Sodium cyanoborohydride Sigma-Aldrich Cat# 156159 DMSO Sigma-Aldrich Cat# D2438 Acetic acid Fisher Scientific Cat# 10384970 PNGase F New England BioLabs Cat# P0705S Endoglycosidase H New England BioLabs Cat# P0702S PNGase A New England BioLabs Cat# P0707S Critical Commercial Assays Pierce Fab Preparation Kit Thermo Scientific Cat# 44985 Deposited Data CryoEM map of native SINV-EEEV chimera (4.4Å) This paper EMD-9280 CryoEM map of native SINV-EEEV chimera showing N-terminal chain (4.8Å) This paper EMD-9281 CryoEM map of SINV-EEEV chimera with Fab of EEEV-3 This paper EMD-9274 CryoEM map of SINV-EEEV chimera with Fab of EEEV-5 This paper EMD-9275 CryoEM map of SINV-EEEV chimera with Fab of EEEV-42 This paper EMD-9249 CryoEM map of SINV-EEEV chimera with Fab of EEEV-58 This paper EMD-9278 CryoEM map of SINV-EEEV chimera with Fab of EEEV-69 This paper EMD-9279 Coordinates of E1-E2-capsid protein for native SINV-EEEV cryoEM map This paper PDB ID 6MX4 Coordinates of capsid protein for native SINV-EEEV cryoEM map This paper PDB ID 6MX7 Coordinates of E1-E2 ecto-domains and fitted Fab homolog in SINV-EEEV: EEEV-3 cryoEM map This paper PDB ID 6MW9 Coordinates of E1-E2 ecto-domains and fitted Fab homolog in SINV-EEEV: EEEV-5 cryoEM map This paper PDB ID 6MWC Coordinates of E1-E2 ecto-domains and fitted Fab homolog in SINV-EEEV: EEEV-42 cryoEM map This paper PDB ID 6MUI Coordinates of E1-E2 ecto-domains and fitted Fab homolog in SINV-EEEV: EEEV-58 cryoEM map This paper PDB ID 6MWV Coordinates of E1-E2 ecto-domains and fitted Fab homolog in SINV-EEEV: EEEV-69 cryoEM map This paper PDB ID 6MWX (Continued on next page) e1 Cell Reports 25, 3136–3147.e1–e5, December 11, 2018 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental Models: Cell Lines African green monkey kidney (Vero) cell WHO Reference Cell Bank WHO Vero cells Baby Hamster Kidney (BHK)-15 cells Kuhn Lab (Purdue University) N/A Aedes albopictus C6/36 ATCC Cat#CRL-1660 Raji B cells expressing DC-SIGN Kwon et al., 2002 N/A Raji B cells expressing L-SIGN Kwon et al., 2002 N/A Raji B cells Kwon et al., 2002 N/A Software and Algorithms Prism GraphPad Software Prism Version 7.0d Empower 3.0 Waters N/A NetNGlyc 1.0 http://www.cbs.dtu.dk/ services/NetNGlyc/ N/A Leginon Carragher et al., 2000 N/A Motioncor2 Zheng et al., 2017 N/A CTFFIND4 Rohou and Grigorieff, 2015 N/A Appion Lander et al., 2009 N/A Relion Scheres, 2012 N/A jspr Guo and Jiang, 2014 N/A ResMap Kucukelbir et al., 2014 N/A Phenix Real Space Refine Adams et al., 2010 N/A Rosetta Alford et al., 2017 N/A MolProbity Chen et al., 2010 N/A COOT Emsley and Cowtan, 2004 N/A PyMol https://pymol.org/2/ N/A Chimera Pettersen et al., 2004 N/A RIVEM Xiao and Rossmann, 2007 N/A EMfit Rossmann et al., 2001 N/A I-TASSER Yang et al., 2015 N/A Clustal Omega Sievers et al., 2011 N/A ESpript Gouet et al., 2003 N/A ExPasy Gasteiger et al., 2003 N/A Other Spe-ed Amide 2 cartridges Applied Separations Cat# 4821 Glycan BEH Amide column (2.1 mm x 100 mm, 1.7 mM) Waters Cat# 186004741 PVDF protein-binding membrane Millipore Cat# MAIPS4510 Ultrathin continuous carbon grids Ted Pella Cat# 01824
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