Journal: Cell

Article Title: Structural and Proteomic Characterization of the Initiation of Giant Virus Infection

doi: 10.1016/j.cell.2020.04.032

Figure Lengend Snippet: (Row I) 2D cryoelectron micrographs of particles following either no treatment (A) or post-incubation with pH 2 (E), 100°C (I), or both pH 2 + 100°C (M). (Row II) Central slices (z = 20) of cryoelectron tomograms of particles following either no treatment (B) or post-incubation with pH 2 (F), 100°C (J), or both pH 2 + 100°C (N). (Row III) Central slices of cryo-tomograms with key features highlighted. Blue, distal tips of the external fiber layer; cyan, starfish seal complex; dark gray, dsDNA; red, capsid; yellow, lipid membranes (nucleocapsid). Slices are shown for virions following either no treatment (C) or post-incubation with pH 2 (G), 100°C (K), or both pH 2 + 100°C (O). (Row IV) Scanning electron micrographs of particles in various stages of genome release following either no treatment (D) or post-incubation with pH 2 (H), 100°C (L), or both pH 2 + 100°C (P). See Videos S2, S3, S4, S5, S6, S7, S8, and S9 for videos of the tomograms and tilt series. See EMD-20745–20748 for tomogram volumes.

Article Snippet: ​ REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and Virus Strains Samba Virus Campos et al., 2014 N/A Tupanvirus soda lake Abrahão et al., 2018 N/A Antarctica virus Andrade et al., 2018 N/A Mimivirus strain M4 Boyer et al., 2011 N/A Biological Samples Acanthamoeba castellanii ATCC ATCC 30010 Chemicals, Peptides, and Recombinant Proteins Sodium phosphate, dibasic Sigma-Aldrich Cat # S9390 Urea VWR Life Sciences Cat # 0568 Guanidinium Hydrochloride Amresco Cat #0118 Triton X-100 Alfa Aesar Cat # A16046 Chloroform EMD Cat # CX1055 Dimethyl sulfoxide JT Baker Cat # 9924-01 Bromelain (from pineapple) Sigma Cat # 647-005-00-X Proteinase K Roche Cat #03115879001 DNase I Roche Cat # 10104159001 Lysozyme Amresco Cat # 0663-5G 712 PYG ATCC N/A Sucrose JT Baker Cat # 4072-05 Software and Algorithms IMOD Mastronarde and Held, 2017 https://bio3d.colorado.edu/imod/download.html SerialEM Mastronarde, 2005 https://bio3d.colorado.edu/SerialEM/download.html Leginon Suloway et al., 2005 http://nramm.nysbc.org/downloads/ Amira ThermoFischer Scientific https://www.thermofisher.com/us/en/home/industrial/electron-microscopy/electron-microscopy-instruments-workflow-solutions/3d-visualization-analysis-software/amira-life-sciences-biomedical.html MaxQuant Cox and Mann, 2008 https://www.maxquant.org/ Andromeda Cox et al., 2011 http://coxdocs.org/doku.php?id=maxquant:start/ MotionCor2 Zheng et al., 2017 https://msg.ucsf.edu/software Other Quantifoil R2/2 Grids Electron Microscopy Sciences Cat # Q250-CR2 10 nm Nanogold Fiducial Markers Aldrich (Millipore) Cat #741957 VSWP Membrane Filter Discs Millipore Cat # VSWP01300 Quantifoil R3.5/1 Grids Electron Microscopy Sciences Cat # Q225CR-35 Deposited Data Generated pH 2 treated sample, Video S3 This work EMDB: EMD-20747 100°C treated sample, Video S4 This work EMDB: EMD-20748 pH 2 + 100°C treated sample, Video S6 This work EMDB: EMD-20746 pH 2 + 100°C treated sample, Video S8 This work EMDB: EMD-20745 Open in a separate window KEY RESOURCES TABLE Giant virus infection intermediates characterized by cryo-EM, cryo-ET, and SEM Proteomics reveal proteins released from capsids during infection Low pH treatment releases proteins present in the viral seed Low pH and high temperature fully open the stargate and release the genome

Techniques: Incubation

Journal: Cell

Article Title: Structural and Proteomic Characterization of the Initiation of Giant Virus Infection

doi: 10.1016/j.cell.2020.04.032

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: ​ REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and Virus Strains Samba Virus Campos et al., 2014 N/A Tupanvirus soda lake Abrahão et al., 2018 N/A Antarctica virus Andrade et al., 2018 N/A Mimivirus strain M4 Boyer et al., 2011 N/A Biological Samples Acanthamoeba castellanii ATCC ATCC 30010 Chemicals, Peptides, and Recombinant Proteins Sodium phosphate, dibasic Sigma-Aldrich Cat # S9390 Urea VWR Life Sciences Cat # 0568 Guanidinium Hydrochloride Amresco Cat #0118 Triton X-100 Alfa Aesar Cat # A16046 Chloroform EMD Cat # CX1055 Dimethyl sulfoxide JT Baker Cat # 9924-01 Bromelain (from pineapple) Sigma Cat # 647-005-00-X Proteinase K Roche Cat #03115879001 DNase I Roche Cat # 10104159001 Lysozyme Amresco Cat # 0663-5G 712 PYG ATCC N/A Sucrose JT Baker Cat # 4072-05 Software and Algorithms IMOD Mastronarde and Held, 2017 https://bio3d.colorado.edu/imod/download.html SerialEM Mastronarde, 2005 https://bio3d.colorado.edu/SerialEM/download.html Leginon Suloway et al., 2005 http://nramm.nysbc.org/downloads/ Amira ThermoFischer Scientific https://www.thermofisher.com/us/en/home/industrial/electron-microscopy/electron-microscopy-instruments-workflow-solutions/3d-visualization-analysis-software/amira-life-sciences-biomedical.html MaxQuant Cox and Mann, 2008 https://www.maxquant.org/ Andromeda Cox et al., 2011 http://coxdocs.org/doku.php?id=maxquant:start/ MotionCor2 Zheng et al., 2017 https://msg.ucsf.edu/software Other Quantifoil R2/2 Grids Electron Microscopy Sciences Cat # Q250-CR2 10 nm Nanogold Fiducial Markers Aldrich (Millipore) Cat #741957 VSWP Membrane Filter Discs Millipore Cat # VSWP01300 Quantifoil R3.5/1 Grids Electron Microscopy Sciences Cat # Q225CR-35 Deposited Data Generated pH 2 treated sample, Video S3 This work EMDB: EMD-20747 100°C treated sample, Video S4 This work EMDB: EMD-20748 pH 2 + 100°C treated sample, Video S6 This work EMDB: EMD-20746 pH 2 + 100°C treated sample, Video S8 This work EMDB: EMD-20745 Open in a separate window KEY RESOURCES TABLE Giant virus infection intermediates characterized by cryo-EM, cryo-ET, and SEM Proteomics reveal proteins released from capsids during infection Low pH treatment releases proteins present in the viral seed Low pH and high temperature fully open the stargate and release the genome

Techniques: Recombinant, Software, Electron Microscopy, Generated