2023-12-13 REL PDBe PDBe PDBe 2021-12-16 2022-02-02 2022-02-02 2023-12-13 European Research Council (ERC) 692637 Germany German Research Foundation (DFG) Schu1080/9-2 Germany Toro-Nahuelpan M Plitzko JM Schueler D Pfeiffer D PopZ, Alphaproteobacteria, cytoskeleton, polarity, CELL CYCLE Toro-Nahuelpan M Plitzko JM Schueler D Pfeiffer D J Mol Biol UK 434 167423 2022 34971672 doi:10.1016/j.jmb.2021.167423 1089-8638 0070 JMOBAK EMD-14021 other EM volume Magnetospirillum gryphiswaldense (wild-type) overproducing PopZ-Mgr Magnetospirillum gryphiswaldense (wild-type) overproducing PopZ-Mgr 0

Individual segmented structures are depicted using different colors in the EMDB entry page image and in the corresponding publication: Putative PopZ filaments are depicted in white. MamK filaments are green. The flagellum is colored in gold. The cellular envelope inner and outer membranes are depicted in blue.

Magnetospirillum gryphiswaldense MSR-1 PopZ 1

The polar organizing protein Z (PopZ) forms a polar microdomain that is inaccessible to larger macromolecules such as ribosomes, and selectively sequesters proteins crucial for cell cycle control and polar morphogenesis in various Alphaproteobacteria. In the present strain PopZ overproduction was achieved via insertion of a Tn5-Ptet-based popZ overexpression cassette into the genome of the Magnetospirillum gryphiswaldense wild-type strain.

Magnetospirillum gryphiswaldense MSR-1 MamK 1

The filament-forming bacterial actin MamK is important for organizing magnetosome organelles into chains that are used for navigation along geomagnetic field lines. Magnetosomes are membranous organelles containing nanometer-sized crystals of magnetite present in magnetotactic bacteria.

Magnetospirillum gryphiswaldense MSR-1 Cellular envelope 1

inner and outer membranes

Magnetospirillum gryphiswaldense MSR-1 Flagellum 1

Flagella are helical protein filaments powered by a rotary motor to mediate motility of bacteria.

Magnetospirillum gryphiswaldense MSR-1 tomography cell 7.0

modified flask standard medium (FSM)

Quantifoil R2/1 MOLYBDENUM CARBON HOLEY GLOW DISCHARGE ETHANE

The mixture was blotted and embedded in vitreous ice by plunge freezing into liquid ethane (< - 170 C). The grids were stored in sealed boxes in liquid nitrogen until used..

Sigma-Aldrich 15 NO SECTIONING FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.5 0.5

Tomography was performed under low-dose conditions using a Titan Krios transmission electron microscope (FEI) equipped with a 300 kV field emission gun, and a Gatan Quantum post-column energy filter. Tilt series were acquired using Serial EM software. The specimen was tilted about one axis with 1.5 degree increments over a typical total angular range of -+ 60 degree. To account for the increased specimen thickness at high tilt angles, the exposure time was multiplied by a factor of 1/cos alpha.

GATAN K2 SUMMIT (4k x 4k) COUNTING 1.5

Data collection was performed at 300 kV, with the energy filter operated in the zero-loss mode (slit width of 20 eV). The cumulative electron dose during the tilt series was kept below 150 e- A-2.

1

Tomograms were reconstructed with (15 nm gold fiducials) the IMOD software package (https://bio3d.colorado.edu/imod/) and treated with an anisotropic non-linear diffusion denoising algorithm to improve signal-to-noise ratio (K: 1, Iterations: 10). Segmentation was performed using Amira software on binned volumes with a voxel size of 10.48 A and 13.68 A. Filaments were traced in Amira using an automated segmentation algorithm based on a generic cylinder as a template implemented in the X-Tracing extension. Prior to filament tracing, binned volumes were subjected to nonlocal-means filtering using Amira software (Thermo Fisher Scientific). The cylindrical templates were generated with a diameter and length of 6 and 15 nm, respectively. To reduce background noise, short filamentous structures with lengths below 30 nm were filtered out. Membrane segmentation was done using the software TomoSegMemTV and a complementary package, SynapSegTools, both for Matlab, and refined manually in Amira (Thermo Fisher Scientific).

321 emd_14022_msk_1.map