REL PDBe PDBe PDBe 2013-04-17 2013-04-24 2013-08-14 2013-08-21 CryoEM reconstruction of the bacteriophage phi6 procapsid to the near-atomic resolution Nemecek D Boura E Wu W Cheng N Plevka P Qiao J Mindich L Heymann JB Hurley JH Steven AC Bacteriophage phi6, Cystoviridae, capsid structure, capsid expansion, segmented genome, conformational change, RNA packaging Nemecek D Boura E Wu W Cheng N Plevka P Qiao J Mindich L Heymann JB Hurley JH Steven AC Subunit folds and maturation pathway of a dsRNA virus capsid. STRUCTURE 21 1374 1383 2013 23891288 doi:10.1016/j.str.2013.06.007 4btg FULLOVERLAP Wildtype P1247 procapsid of bacteriophage phi6 Wildtype P1247 procapsid of bacteriophage phi6 icosahedral shell with accessory proteins 4 12.6 Pseudomonas phage phi6 Pseudomonas phage phi6 Pseudomonas syringae BACTERIA(EUBACTERIA) Escherichia coli JM109 pLM687 12.6 P1247 450 2 VIRION SPECIES false true bacteriophage phi-6 singleParticle particle 10 8.0
10 mM potassium phosphate, 5 mM MgCl2
400 mesh C-flat holey carbon grid
 ETHANE 80 100 FEI VITROBOT MARK I Blot for 2 seconds before plunging. FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 0.8 2.2 46000.0 44739.0 FEI TITAN KRIOS AUTOGRID HOLDER 2011-11-20 KODAK SO-163 FILM NIKON SUPER COOLSCAN 9000 6.35 220 15 16. 0 0
The particles were selected using e2boxer (EMAN) and manually pruned in bshow (BSOFT). The initial model was taken from our previous reconstruction at 7A resolution (EMD-2341). The final structure was reconstructed in EMAN.
Particles from each micrograph
 I 4.4 FSC 0.5 CUT-OFF EMAN, BSOFT 18326 emd_2364.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 420 420 420 -210 -210 -210 420 420 420 586.74 586.74 586.74 90.0 90.0 90.0 X Y Z -8.04054451 21.12542534 0.0 1.0 1.397 1.397 1.397 2.0 AUTHOR Reconstruction of the wildtype P1247 procapsid of bacteriophage phi6
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 4K7H A FLEXIBLE FIT Chimera, MDFF, Coot
the P1 crystal structure was rigid body-fitted into the procapsid map using Chimera. Regions where the crystal structure deviated significantly from the EM density were roughly adjusted in Coot and then the P1A and P1B structures were flexibly fitted using the MDFF package. Finally, both structures were visually inspected and refined in Coot.
REAL
emd_2364.jpg
emd_2364_msk_2.map emd_2364_msk_2.map 1 IMAGE STORED AS SIGNED BYTE 420 420 420 -210 -210 -210 420 420 420 586.74 586.74 586.74 90.0 90.0 90.0 X Y Z 0.0 1.0 0.00070122 0.02647128 1.397 1.397 1.397 This mask represents the P1A subunit
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 emd_2364_msk_1.map emd_2364_msk_1.map 1 IMAGE STORED AS SIGNED BYTE 420 420 420 -210 -210 -210 420 420 420 586.74 586.74 586.74 90.0 90.0 90.0 X Y Z 0.0 1.0 0.00070345 0.02651325 1.397 1.397 1.397 This mask represents the P1B subunit
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 emd_2364_fsc.xml