2024-07-10 REL PDBe PDBe PDBe 2021-05-01 2022-02-09 2022-02-09 2024-07-10 Biotechnology and Biological Sciences Research Council (BBSRC) BB/N005570/1 United Kingdom Model of closed pentamer of the Haliangium ochraceum encapsulin from symmetry expansion of icosahedral single particle reconstruction Marles-Wright J Basle A Encapsulin, encapsulated ferritin, haliangium ochraceum, VIRUS LIKE PARTICLE 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 Marles-Wright J Basle A Clarke DJ Ross J Model of Haliangium ochraceum encapsulin from icosahedral single particle reconstruction Biorxiv US 2021 doi:10.1101/2021.04.15.439977 2692-8205 0353 7oe2 FULLOVERLAP 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 1.8 Linocin_M18 bacteriocin protein Haliangium ochraceum (strain DSM 14365 / JCM 11303 / SMP-2) DSM 14365 / JCM 11303 / SMP-2 0.028844598 5 Escherichia coli BL21(DE3) LEVO MDLLKRHLAPIVPDAWSAIDEEAKEIFQGHLAGRKLVDFRGPFGWEYAAVNTGELRPIDDTPEDVDMKLRQVQPLAEVRV PFTLDVTELDSVARGATNPDLDDVARAAERMVEAEDSAIFHGWAQAGIKGIVDSTPHEALAVASVSDFPRAVLSAADTLR KAGVTGPYALVLGPKAYDDLFAATQDGYPVAKQVQRLVVDGPLVRANALAGALVMSMRGGDYELTVGQDLSIGYAFHDRS KVELFVAESFTFRVLEPGAAVHLRYA D0LZ74 Haliangium ochraceum Encapsulated ferritin localisation sequence Haliangium ochraceum (strain DSM 14365 / JCM 11303 / SMP-2) DSM 14365 / JCM 11303 / SMP-2 0.014817368 5 Escherichia coli BL21(DE3) LEVO MSSEQLHEPAELLSEETKNMHRALVTLIEELEAVDWYQQRADACSEPGLHDVLIHNKNEEVEHAMMTLEWIRRRSPVFDA HMRTYLFTERPILELEEEDTGSSSSVAASPTSAPSHGSLGIGSLRQEGKED D0LZ73 water 1.8015e-05 154 HOH 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) 11520 8184 1 8109 1.0 40.509 1 340403 1 FOURIER SPACE 2.4 FSC 0.143 CUT-OFF RELION 3.1 4734551 MAXIMUM LIKELIHOOD RELION 3.1 Initial model
Initial model produced in Relion
 MAXIMUM LIKELIHOOD RELION 3.1 3 254134.0 RELION 3.1
Final 3D classification used to remove broken particles.
 emd_12859.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 576 576 576 0 0 0 576 576 576 375.552 375.552 375.552 90.0 90.0 90.0 X Y Z -0.010531169 0.028896166 -0.00039376642 0.0014212929 0.652 0.652 0.652 0.01 AUTHOR Refine 3D map RIGID BODY FIT
Initial fitting performed using chimera with real space refinement in Phenix.
CC REAL 86.0 emd_12859_msk_1.map emd_12859_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 576 576 576 0 0 0 576 576 576 375.552 375.552 375.552 90.0 90.0 90.0 X Y Z -0.100344375 0.14196405 0.00003072598 0.0019059828 0.652 0.652 0.652 AUTHOR Post processed masked map emd_12859_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 576 576 576 0 0 0 576 576 576 375.552 375.552 375.552 90.0 90.0 90.0 X Y Z -0.010540561 0.029276982 -0.00039395044 0.0014449453 0.652 0.652 0.652 AUTHOR Half 1 emd_12859_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 576 576 576 0 0 0 576 576 576 375.552 375.552 375.552 90.0 90.0 90.0 X Y Z -0.010525077 0.028894158 -0.00039365335 0.0014449834 0.652 0.652 0.652 AUTHOR Half 2