2022-02-09 REL PDBe PDBe PDBe 2021-09-20 2022-02-09 2022-02-09 2022-02-09 Biotechnology and Biological Sciences Research Council (BBSRC) BB/N005570/1 United Kingdom Asymmetric single particle reconstruction of the Haliangium ochraceum encapsulin encapsulated ferritin complex calculated using Cryosparc Marles-Wright J Basle A Ross J Clarke DJ Ross J McIver Z Lambert T Piergentili C Bird JE Gallagher KJ Cruickshank FL James P Zarazua-Arvizu E Horsfall LE Waldron KJ Wilson MD Mackay CL Basle A Clarke DJ Marles-Wright J Pore dynamics and asymmetric cargo loading in an encapsulin nanocompartment. Sci Adv US 8 eabj4461 eabj4461 2022 35080974 doi:10.1126/sciadv.abj4461 2375-2548 EMD-13603 associated EM volume Ternary complex of Haliangium ochraceum encapsulin and encapsulated ferritin proteins Ternary complex of Haliangium ochraceum encapsulin and encapsulated ferritin proteins 0 1 2
Complex produced by co-expression in E. coli
Haliangium ochraceum Escherichia coli BL21(DE3) 1.8 Haliangium ochraceum encapsulin Haliangium ochraceum Escherichia coli BL21(DE3) LEVO MDLLKRHLAPIVPDAWSAIDEEAKEIFQGHLAGRKLVDFRGPFGWEYAAVNTGELRPIDD TPEDVDMKLRQVQPLAEVRVPFTLDVTELDSVARGATNPDLDDVARAAERMVEAEDSAIF HGWAQAGIKGIVDSTPHEALAVASVSDFPRAVLSAADTLRKAGVTGPYALVLGPKAYDDL FAATQDGYPVAKQVQRLVVDGPLVRANALAGALVMSMRGGDYELTVGQDLSIGYAFHDRS KVELFVAESFTFRVLEPGAAVHLRYA Haliangium ochraceum encapsulated ferritin Haliangium ochraceum Escherichia coli BL21(DE3) LEVO MSSEQLHEPAELLSEETKNMHRALVTLIEELEAVDWYQQRADACSEPGLHDVLIHNKNEE VEHAMMTLEWIRRRSPVFDAHMRTYLFTERPILELEEEDTGSSSSVAASPTSAPSHGSLG IGSLRQEGKED singleParticle particle 3 8.0 150.0 NaCl Sodium chloride 20.0 HEPES
Solutions were prepared with MilliQ water and filtered using a 0.22 um filter.
 Quantifoil GOLD 200 CARBON HOLEY GLOW DISCHARGE AIR ETHANE 100 281 FEI VITROBOT MARK IV
blot force -5, wait time 10 seconds and blot time of 3 seconds.
Sample mono disperse as determined by SEC
 FEI TITAN KRIOS OTHER BRIGHT FIELD FIELD EMISSION GUN 300 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K3 (6k x 4k) 1150 8184 1 8109 1.0 40.509 1 2239839
Particles initially picked from a limited set of micrographs with blob picker in CryoSPARC then 2D references produced for further rounds of Template Based autopicking. Successive rounds of 2D classification were used to select particles in well-defined classes
 CTFFIND 2
CTF correction after motion correction
 1 C1 FOURIER SPACE 3.24 FSC 0.143 CUT-OFF cryoSPARC 3.2 333945 MAXIMUM LIKELIHOOD cryoSPARC 3.2
Initial model produced in Cryosparc
 MAXIMUM LIKELIHOOD cryoSPARC 3.2 5 50000.0 cryoSPARC
Five models generated for ab initio stage followed by heterogeneous refinement of these five models.
 emd_13603.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 312.96 312.96 312.96 90.0 90.0 90.0 X Y Z -0.06601886 0.20806196 0.0031889973 0.015094721 0.652 0.652 0.652 0.05 AUTHOR cryosparc map emd_13603_msk_1.map emd_13603_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 312.96 312.96 312.96 90.0 90.0 90.0 X Y Z -0.25760415 0.5111953 0.0031887623 0.027130842 0.652 0.652 0.652 AUTHOR sharpened map emd_13603_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 312.96 312.96 312.96 90.0 90.0 90.0 X Y Z -0.27925038 0.39522767 0.0025138007 0.05150839 0.652 0.652 0.652 AUTHOR Half map B emd_13603_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 312.96 312.96 312.96 90.0 90.0 90.0 X Y Z -0.28412738 0.35799846 0.0025125947 0.051530503 0.652 0.652 0.652 AUTHOR Half map A