2024-05-15 REL PDBe PDBe PDBe 2018-07-13 2018-10-24 2018-10-31 2024-05-15 Medical Research Council (United Kingdom) MC_UU_12014/7 United Kingdom Structure of the Macrobrachium rosenbergii Nodavirus Ho KH Gabrielsen M Nodavirus, Capsid, Virion, VIRUS LIKE PARTICLE Ho KL Gabrielsen M Beh PL Kueh CL Thong QX Streetley J Tan WS Bhella D Structure of the Macrobrachium rosenbergii nodavirus: A new genus within the Nodaviridae? PLoS Biol. US 16 e3000038 e3000038 2018 30346944 doi:10.1371/journal.pbio.3000038 1545-7885 EMD-3655 other EM volume
Previously solved structure at lower resolution
 6h2b FULLOVERLAP Macrobrachium rosenbergii nodavirus Macrobrachium rosenbergii nodavirus 0 1
Capsid protein was expressed in Sf9 cells
Macrobrachium rosenbergii nodavirus Macrobrachium rosenbergii Capsid 400.0 3 VIRUS-LIKE PARTICLE OTHER false false Capsid protein Macrobrachium rosenbergii nodavirus 0.041563593999999995 3 Spodoptera frugiperda LEVO MARGKQNSNQAQNNSNANGKRRKRSRRNRNPQTIPNFNPIVAKPTVAPLQTNIRSARSDVNAITVLNGSDFLTTVKVRGS NNLTDSKSRILVKQPISASSFLGTRISGLSQFWERYRWHKAAVRYVPAVPNTLACQLIGYIDTDPLDDPNVILDVDQLLR QATSQVGARQWNFSDTTTIPLIVRRDDQLYYTGQDKENVRFSQQGVFYLLQVTTLLNISGEAITNDLISGSLYLDWVCGF SMPQINPTPVEISQLTYNADTIGNWVPPTELNQTYTQDITGLKPNSKFIIVPYMDRTSSEVLQKCTITCNEVNAVGSISY FDTNDIKCNGYITFQANNIGEATFTLVTDYKGVTDAKPYQYRIIRAIVGNN X2FE19 CALCIUM ION 4.0078e-05 6 CA singleParticle particle 0.2 7.4
20 mM HEPES, 100 mM NaCl pH 7.4
 Quantifoil R2/2 COPPER 400 CARBON CONTINUOUS GLOW DISCHARGE AIR ETHANE 100 277
VLPs were deposited onto a continuous carbon film that had been floated onto a quantifoil holey carbon film (R2/2).
FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.0 2.5 47170.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum 20 GATAN K2 QUANTUM (4k x 4k) COUNTING 2-20 1 2459 5.0 36.0 1 60939
Automated particle picking in Relion 2.1
 EMD-3655
our previously calculated intermediate resolution structure of the same VLP was used to start data processing.
 I BACK PROJECTION 3.28 FSC 0.143 CUT-OFF RELION 2.1
Standard Relion workflow for icosahedral particle.
40883 PROJECTION MATCHING RELION 2.1 PROJECTION MATCHING RELION 2.1 RELION emd_0129.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 -256 -256 -256 512 512 512 542.72 542.72 542.72 90.0 90.0 90.0 X Y Z -0.08820353 0.15871026 0.00086273794 0.006595679 1.06 1.06 1.06 0.02 AUTHOR None AB INITIO MODEL
Model 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.
REAL 140.0