2019-12-18RELPDBePDBePDBe2018-07-132018-10-242018-10-312019-12-18Medical Research Council (United Kingdom)MC_UU_12014/7United KingdomStructure of the Macrobrachium rosenbergii NodavirusHo KHGabrielsen MBeh PLKueh CLThong QXStreetley JTan WSBhella DHo KLGabrielsen MBeh PLKueh CLThong QXStreetley JTan WSBhella DStructure of the Macrobrachium rosenbergii nodavirus: A new genus within the Nodaviridae?PLoS Biol.US16e3000038e3000038201830346944doi:10.1371/journal.pbio.30000381545-7885EMD-3655other EM volumePreviously solved structure at lower resolutionEMD-0129associated EM volumeStructure of the Macrobrachium rosenbergii Nodavirus6h2bFULLOVERLAPMacrobrachium rosenbergii nodavirusMacrobrachium rosenbergii nodavirus01Capsid protein was expressed in Sf9 cellsMacrobrachium rosenbergii nodavirusMacrobrachium rosenbergiiSpodoptera frugiperdaCapsid400.03VIRUS-LIKE PARTICLEOTHERfalsefalseCapsid proteinMacrobrachium rosenbergii nodavirus0.0415635943Spodoptera frugiperdaLEVOMARGKQNSNQAQNNSNANGKRRKRSRRNRNPQTIPNFNPIVAKPTVAPLQTNIRSARSDVNAITVLNGSDFLTTVKVRGS
NNLTDSKSRILVKQPISASSFLGTRISGLSQFWERYRWHKAAVRYVPAVPNTLACQLIGYIDTDPLDDPNVILDVDQLLR
QATSQVGARQWNFSDTTTIPLIVRRDDQLYYTGQDKENVRFSQQGVFYLLQVTTLLNISGEAITNDLISGSLYLDWVCGF
SMPQINPTPVEISQLTYNADTIGNWVPPTELNQTYTQDITGLKPNSKFIIVPYMDRTSSEVLQKCTITCNEVNAVGSISY
FDTNDIKCNGYITFQANNIGEATFTLVTDYKGVTDAKPYQYRIIRAIVGNNCALCIUM ION4.0078e-056CAsingleParticleparticle0.27.420 mM HEPES, 100 mM NaCl pH 7.4Quantifoil R2/2COPPER400CARBONCONTINUOUSGLOW DISCHARGEAIRETHANE100277VLPs were deposited onto a continuous carbon film that had been floated onto a quantifoil holey carbon film (R2/2). FEI TITAN KRIOSFLOOD BEAMBRIGHT FIELDFIELD EMISSION GUN3001.02.547170.0FEI TITAN KRIOS AUTOGRID HOLDERNITROGENGIF Bioquantum20GATAN K2 QUANTUM (4k x 4k)COUNTING2-20124595.036.0160939Automated particle picking in Relion 2.1RELION2.1EMD-3655our previously calculated intermediate resolution structure of the same VLP was used to start data processing.IBACK PROJECTION3.28FSC 0.143 CUT-OFFRELION2.1Standard Relion workflow for icosahedral particle.40883PROJECTION MATCHINGRELION2.1PROJECTION MATCHINGRELION2.1RELIONAB INITIO MODELModel built largely ab initio, following docking of a homology model based on PDB 4LLF. The homology model matched in two strands at residues - 104-135 and 232-243. This served as the starting point for manual model building. The model was then subjected to real space refinement using Phenix.REAL140