EMPIAR-10885 - In vivo architecture of the polar organizing protein Z (PopZ) meshwork in the Alphaproteobacteria Magnetospirillum gryphiswaldense and Caulobacter crescentus [multiple data sets in MRC format]

EMPIAR-10885

In vivo architecture of the polar organizing protein Z (PopZ) meshwork in the Alphaproteobacteria Magnetospirillum gryphiswaldense and Caulobacter crescentus [multiple data sets in MRC format]

Publication:

In vivo architecture of the polar organizing protein Z (PopZ) meshwork in the Alphaproteobacteria Magnetospirillum gryphiswaldense and Caulobacter crescentus

Toro-Nahuelpan M, Plitzko JM, Schüler D, Pfeiffer D

Journal of molecular biology 434 (2022)

PMID: 34971672

DOI: 10.1016/j.jmb.2021.167423

Related EMDB entry:

EMD-14022 EMD-14021

Deposited:

2021-12-16

Released:

2022-01-12

Last modified:

2022-02-10

Imageset size:

6.43 GB

Imageset DOI:

10.6019/EMPIAR-10885

Experimental metadata:

Download xml json

Contains:

reconstructed volumes

Image Sets

1. Volta phase plate cryo-electron tomography of Magnetospirillum gryphiswaldense (wild-type) overproducing PopZ-Mgr

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

Image size:

(928, 928)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(13.68, 13.68)

Details:

Reconstructed bin4 tomograms of Magnetospirillum gryphiswaldense (wild-type) overproducing PopZ-Mgr. Tomograms were reconstructed with the IMOD software package and treated with an anisotropic non-linear diffusion denoising algorithm to improve signal-to-noise ratio (K: 1, Iterations: 10). The folder also contains the segmentation data (the respective structures are encoded in the readMe.txt file) and segmentation image snapshots (PopZ filaments are depicted in white and the cellular envelope in blue, MamK filaments are green, Flagella are represented in gold). Fig. 1A, Movie S1, and Movie S2 in the corresponding publication are related to cell1, Fig. S2 is related to cell2. Note, the number of image frames (slices) varies among the micrographs.

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2. Volta phase plate cryo-electron tomography of Magnetospirillum gryphiswaldense delta-mamK overproducing PopZ-Mgr

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

Image size:

(960, None)

Pixel type:

SIGNED BYTE

Pixel spacing:

(13.68, 13.68)

Details:

Reconstructed bin4 tomograms of Magnetospirillum gryphiswaldense delta-mamK overproducing PopZ-Mgr. Tomograms were reconstructed with the IMOD software package and treated with an anisotropic non-linear diffusion denoising algorithm to improve signal-to-noise ratio (K: 1, Iterations: 10). Micrographs are related to the following figures in the corresponding publication: cell_1_bin4_filtered, Fig. S3A; cell_4_bin4_filtered, Fig. S3B, Movie S3; cell_5_bin4_filtered, Fig. S3C. Cell_6_bin4_filtered depicts an additional cell not shown in the publication. Note, image height and number of image frames (slices) vary among the micrographs.

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3. Volta phase plate cryo-electron tomography of purified PopZ-Mgr

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

Image size:

(960, 928)

Pixel type:

SIGNED BYTE

Pixel spacing:

(6.96, 6.96)

Details:

Reconstructed bin4 tomograms of purified PopZ-Mgr (produced recombinantly in Escherichia coli). Tomograms were reconstructed with the IMOD software package and treated with an anisotropic non-linear diffusion denoising algorithm to improve signal-to-noise ratio (K: 1, Iterations: 10). Tomo_16_bin4 is related to the following figures in the corresponding publication: Fig. S6A, Movie S8. Tomo_14_bin4: additional unpublished micrograph. Note, the number of image frames (slices) varies among the micrographs.

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4. Cryo-electron tomography of Magnetospirillum gryphiswaldense delta-popZ overproducing PopZ-Mgr

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

Image size:

(564, 616)

Pixel type:

SIGNED BYTE

Pixel spacing:

(31.32, 31.32)

Details:

Reconstructed and filtered bin6 tomogram of Magnetospirillum gryphiswaldense delta-popZ overproducing PopZ-Mgr. The folder also contains the segmentation data and segmentation image snapshots (Putative PopZ filaments are depicted in purple, MamK filaments are green, Magnetite crystals are red, magnetosome membrane vesicles are yellow, and the cellular envelope inner and outer membranes are depicted in blue). The transition area between the ribosome containing cytoplasm and PopZ dependent ribosome exclusion zone is depicted in turquoise. The data is related to Fig. S4B+C in the corresponding publication.

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5. Volta phase plate cryo-electron tomography of Caulobacter crescentus NA1000

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

Image size:

(640, 620)

Pixel type:

SIGNED BYTE

Pixel spacing:

(20.52, 20.52)

Details:

Reconstructed binned tomograms of Caulobacter crescentus NA1000 (wild-type). Tomograms were reconstructed with the IMOD software package and treated with an anisotropic non-linear diffusion denoising algorithm to improve signal-to-noise ratio (K: 1, Iterations: 10). Micrographs are related to the corresponding figures in the original publication: cell_5, Fig. S5B, Movie S6; cell_11, Movie S7. All other tomograms depict additional cells not shown in the publication. Note, the number of image frames (slices) varies among the micrographs.

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6. Volta phase plate cryo-electron tomography of Caulobacter crescentus NA1000 overproducing PopZ-Cc

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

Image size:

(640, 620)

Pixel type:

SIGNED BYTE

Pixel spacing:

(15.72, 15.72)

Details:

Reconstructed binned tomograms of Caulobacter crescentus NA1000 overproducing PopZ-Cc. Tomograms were reconstructed with the IMOD software package and treated with an anisotropic non-linear diffusion denoising algorithm to improve signal-to-noise ratio (K: 1, Iterations: 10). Micrographs are related to the following figures in the corresponding publication: cell_2.rec, Fig. 1B, Fig. S5A, Movie S4; cell_6.rec, Movie S5. All other tomograms depict additional cells not shown in the publication. Note, the number of image frames (slices) varies among the micrographs.

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Archives and downloads the selected files into an uncompressed zip file.

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7. Cryo-electron tomography of Magnetospirillum gryphiswaldense delta-popZ

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

Image size:

(924, 375)

Pixel type:

SIGNED BYTE

Pixel spacing:

(20.88, 20.88)

Details:

Reconstructed bin4 tomogram of Magnetospirillum gryphiswaldense delta-popZ. The micrograph is related to Fig. S4A in the publication.

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Archives and downloads the selected files into an uncompressed zip file.

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8. Volta phase plate cryo-electron tomography of Magnetospirillum gryphiswaldense delta-mamK-mamY

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

Image size:

(640, 620)

Pixel type:

SIGNED BYTE

Pixel spacing:

(15.72, 15.72)

Details:

Reconstructed bin6 tomogram of Magnetospirillum gryphiswaldense delta-mamK-mamY. The micrograph is related to Fig. S3D in the publication.

Files:

Archives and downloads the selected files into an uncompressed zip file.

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