2024-07-10 REL PDBe PDBe PDBe 2019-10-30 2020-01-01 2020-01-01 2024-07-10 Novo Nordisk Foundation NNF17OC0030788 Denmark National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) R01-MH112766 United States Medical Research Council (United Kingdom) MC_UP_1201/16 United Kingdom Structure of the five-fold capsomer of the dArc2 capsid Erlendsson S Morado DR dArc, Gag, Virus, VLP, VIRUS LIKE PARTICLE Erlendsson S Morado DR Cullen HB Feschotte C Shepherd JD Briggs JAG Structures of virus-like capsids formed by the Drosophila neuronal Arc proteins. Nat.Neurosci. US 23 172 175 2020 31907439 doi:10.1038/s41593-019-0569-y 1097-6256 6tat FULLOVERLAP dArc2 Capsids dArc2 Capsids 0 1
The five-fold dArc2 capsomer map is generated by symmetry expansion, sub-boxing and local refinement.
Drosophila melanogaster Activity-regulated cytoskeleton associated protein 2 Drosophila melanogaster 0.022656733999999998 5 Escherichia coli LEVO MTQMSDEQFRIFIETIKSLGPIKEEPPSKGSFSNCTVRFSGQRDHDAVDEFINAVETYKEVEGISDKDALKGLPLLFKSI AVVWWKGVRRDAKTWSDALQLLRDHFSPTKPSYQIYMEIFETKQSYDEVIDSFICKQRALLAKLPEGRHDEETELDFIYG LMQPKYRESIPRHEVKTFRELLDRGRTVERTRH Q7JV70 singleParticle particle 0.1 8.0 150.0 NaCl sodium chloride 50.0 C4H11NO3 Tris 1.0 C4H10O2S2 DTT 50.0 ZnCl2 zinc cloride Homemade COPPER 300 CARBON LACEY CARBON CONTINUOUS GLOW DISCHARGE AIR 0.039
25 mA
 ETHANE 100 278 FEI VITROBOT MARK IV
dArc2 capsids
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 0.8 3.0 105000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum 20 GATAN K2 SUMMIT (4k x 4k) COUNTING 4096 4096 1-75 35.0 1 21348
From 1779 initial dArc2 icosahedral capsids, we performed symmetry expansion as implemented in RELION, to calculate the positions and orientations for each of the 106,740 asymmetric units for dArc2, centered at the five-fold capsomeres. We extracted individual capsomeres using a box size of 148 pixels. For the five-fold capsomeres we removed the redundant five-fold symmetrized capsomeres leaving 21,348 particles.
 C5 FOURIER SPACE 3.7 FSC 0.143 CUT-OFF RELION 3 21348 MAXIMUM LIKELIHOOD RELION 3 MAXIMUM LIKELIHOOD RELION 3 emd_10427.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 148 148 148 0 0 0 148 148 148 205.424 205.424 205.424 90.0 90.0 90.0 X Y Z -0.007047234 0.44123968 0.0015141699 0.013864755 1.388 1.388 1.388 0.05 AUTHOR dArc2 five-fold capsomer 6GSE PDB experimental model AB INITIO MODEL REAL emd_10427_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 148 148 148 0 0 0 148 148 148 205.424 205.424 205.424 90.0 90.0 90.0 X Y Z -0.017268017 0.05275773 0.0006713419 0.004276149 1.388 1.388 1.388 AUTHOR dArc2 five-fold capsomer unsharpened