2024-03-13 REL RCSB RCSB RCSB 2018-11-06 2018-12-05 2019-03-13 2024-03-13 National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) 5 R01 AI114975-05 United States Department of Energy (DOE, United States) DE-FG01-91ER20021 United States Cryo-EM structure of the HO BMC shell: Icosahedral reconstruction (main population) Greber BJ Sutter M microcompartment, shell, compartmentalization, BMC fold, STRUCTURAL PROTEIN, VIRUS LIKE PARTICLE Greber BJ Sutter M Kerfeld CA The Plasticity of Molecular Interactions Governs Bacterial Microcompartment Shell Assembly. Structure UK 27 749 763.e4 2019 30833088 doi:10.1016/j.str.2019.01.017 0969-2126 2005 STRUE6 EMD-9310 other EM volume EMD-9311 other EM volume EMD-9307 other EM volume EMD-9308 other EM volume EMD-9312 other EM volume EMD-9296 other EM volume EMD-9314 other EM volume EMD-9313 other EM volume EMD-9315 other EM volume 6mzx FULLOVERLAP Bacterial microcompartment shell from Haliangium ochraceum Bacterial microcompartment shell from Haliangium ochraceum 0 1 2 3 Haliangium ochraceum 6.5 Ethanolamine utilization protein EutN/carboxysome structural protein Ccml Haliangium ochraceum (strain DSM 14365 / JCM 11303 / SMP-2) DSM 14365 / JCM 11303 / SMP-2 0.009866318999999998 1 Escherichia coli LEVO MVLGKVVGTVVASRKEPRIEGLSLLLVRACDPDGTPTGGAVVCADAVGAGVGEVVLYASGSSARQTEVTNNRPVDATIMA IVDLVEMGGDVRFRKD D0LHE5 Microcompartments protein HO-5815 Haliangium ochraceum (strain DSM 14365 / JCM 11303 / SMP-2) DSM 14365 / JCM 11303 / SMP-2 0.010126718 6 Escherichia coli LEVO MADALGMIEVRGFVGMVEAADAMVKAAKVELIGYEKTGGGYVTAVVRGDVAAVKAATEAGQRAAERVGEVVAVHVIPRPH VNVDAALPLGRTPGMDKSA D0LID5 Microcompartments protein HO-5816 Haliangium ochraceum DSM 14365 / JCM 11303 / SMP-2 0.022904136999999998 2 Escherichia coli LEVO MSITLRTYIFLDALQPQLATFIGKTARGFLPVPGQASLWVEIAPGIAINRVTDAALKATKVQPAVQVVERAYGLLEVHHF DQGEVLAAGSTILDKLEVREEGRLKPQVMTHQIIRAVEAYQTQIINRNSQGMMILPGESLFILETQPAGYAVLAANEAEK AANVHLVNVTPYGAFGRLYLAGSEAEIDAAAEAAEAAIRSVSGVAQESFRDR D0LID6 singleParticle particle 3 7.4 20.0 Tris-HCl 50.0 Sodium chloride 0.01 NP-40 substitute C-flat-1.2/1.3 COPPER 400 CARBON HOLEY CARBON CONTINUOUS PLASMA CLEANING
Protochips C-flat 1.2/1.3 holey carbon grids were coated with a thin carbon film and plasma cleaned using a Gatain Solarus.
 ETHANE 100 277 FEI VITROBOT MARK IV
5-7 sec incubation of the sample on the grid before blotting and plunging.
FEI TITAN FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 1.0 3.5 48543.0 GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER NITROGEN GATAN K2 SUMMIT (4k x 4k) COUNTING 3838 3710 1-30 1 928 4.5 25.0
928 images retained after inspection for image quality. Frames were aligned and dose weighed using Motioncor2.
 1 31800
1000 particles were picked manually to generate reference templates for subsequent auto-picking in RELION 1.4.
 EMD-8747
The reference was re-scaled and placed in a 512x512x512 voxel box to match the pixel size and appropriate box size for the data.
 1 I FOURIER SPACE 3.0 FSC 0.143 CUT-OFF FREALIGN 9
Frequency-limited refinement in FREALIGN, excluding spatial frequencies higher than 3.6 Angstroms to avoid over-fitting. Icosahedral symmetry was applied throughout the refinement procedure.
15779 MAXIMUM LIKELIHOOD RELION 1.4 PROJECTION MATCHING FREALIGN 9
Final refinement in FREALIGN, using defocus refinement and Ewald sphere correction.
 4 7950.0 RELION 1.4
Icosahedral symmetry was applied during the classification.
 emd_9309.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 527.36 527.36 527.36 90.0 90.0 90.0 X Y Z -0.4511142 0.84809214 0.0040241475 0.042632665 1.03 1.03 1.03 0.1 AUTHOR Cryo-EM reconstruction of the HO BMC shell (icosahedral symmetry) 5V74 PDB experimental model OTHER REAL emd_9309_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 527.36 527.36 527.36 90.0 90.0 90.0 X Y Z -0.0385796 0.12536946 0.0019673323 0.009393815 1.03 1.03 1.03 AUTHOR Unfiltered half-map emd_9309_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 527.36 527.36 527.36 90.0 90.0 90.0 X Y Z -0.03985662 0.13141398 0.001970461 0.009413776 1.03 1.03 1.03 AUTHOR Unfiltered half-map