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- EMDB-14021: Cryo-ET of Magnetospirillum gryphiswaldense delta-popZ overproduc... -

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Basic information

Entry
Database: EMDB / ID: EMD-14021
TitleCryo-ET of Magnetospirillum gryphiswaldense delta-popZ overproducing PopZ-Mgr
Map dataTomogram of Magnetospirillum gryphiswaldense delta-popZ overproducing PopZ-Mgr
Sample
  • Cell: Magnetospirillum gryphiswaldense delta-popZ overproducing PopZ-Mgr
    • Organelle or cellular component: PopZ
    • Organelle or cellular component: Magnetosomes
      • Organelle or cellular component: magnetite crystals
      • Organelle or cellular component: magnetosome membrane vesicles
    • Organelle or cellular component: MamK
    • Organelle or cellular component: Cellular envelope
KeywordsPopZ / Alphaproteobacteria / cytoskeleton / polarity / CELL CYCLE
Biological speciesMagnetospirillum gryphiswaldense MSR-1 (magnetotactic)
Methodelectron tomography / cryo EM
AuthorsToro-Nahuelpan M / Plitzko JM / Schueler D / Pfeiffer D
Funding support Germany, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)692637 Germany
German Research Foundation (DFG)Schu1080/9-2 Germany
CitationJournal: J Mol Biol / Year: 2022
Title: In vivo Architecture of the Polar Organizing Protein Z (PopZ) Meshwork in the Alphaproteobacteria Magnetospirillum gryphiswaldense and Caulobacter crescentus.
Authors: Mauricio Toro-Nahuelpan / Jürgen M Plitzko / Dirk Schüler / Daniel Pfeiffer /
Abstract: 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 ...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. However, the in vivo architecture of this microdomain has remained elusive. Here, we analyzed the three-dimensional ultrastructural organization of the PopZ network in Magnetospirillum gryphiswaldense and Caulobacter crescentus by Volta phase plate cryo-electron tomography, which provides high spatial resolution and improved image contrast. Our results suggest that PopZ forms a porous network of disordered short, flexible, and branching filaments.
History
DepositionDec 16, 2021-
Header (metadata) releaseJan 19, 2022-
Map releaseJan 19, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

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  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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Supplemental images

emd_14021.png

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Map

FileDownload / File: emd_14021.map.gz / Format: CCP4 / Size: 40.1 MB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationTomogram of Magnetospirillum gryphiswaldense delta-popZ overproducing PopZ-Mgr
Voxel sizeX=Y=Z: 31.32 Å
Density
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)-61.271084000000002 (±79.099074999999999)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin57-480
Dimensions616564121
Spacing564616121
CellA: 17664.48 Å / B: 19293.121 Å / C: 3789.7202 Å
α=β=γ: 90.0 °

CCP4 map header:

modeenvelope stored as signed bytes (from -128 lowest to 127 highest)
Å/pix. X/Y/Z31.3231.32000162337731.32
M x/y/z564616121
origin x/y/z0.0000.0000.000
length x/y/z17664.48019293.1213789.720
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS-48570
NC/NR/NS564616121
D min/max/mean-128.000127.000-61.271

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Supplemental data

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Mask #1

Fileemd_14021_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Magnetospirillum gryphiswaldense delta-popZ overproducing PopZ-Mgr

EntireName: Magnetospirillum gryphiswaldense delta-popZ overproducing PopZ-Mgr
Components
  • Cell: Magnetospirillum gryphiswaldense delta-popZ overproducing PopZ-Mgr
    • Organelle or cellular component: PopZ
    • Organelle or cellular component: Magnetosomes
      • Organelle or cellular component: magnetite crystals
      • Organelle or cellular component: magnetosome membrane vesicles
    • Organelle or cellular component: MamK
    • Organelle or cellular component: Cellular envelope

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Supramolecule #1: Magnetospirillum gryphiswaldense delta-popZ overproducing PopZ-Mgr

SupramoleculeName: Magnetospirillum gryphiswaldense delta-popZ overproducing PopZ-Mgr
type: cell / ID: 1 / Parent: 0
Details: Individual segmented structures are depicted in different colors in the EMDB entry image and in the corresponding publication: Putative PopZ filaments are purple. Magnetite crystals are red, ...Details: Individual segmented structures are depicted in different colors in the EMDB entry image and in the corresponding publication: Putative PopZ filaments are purple. Magnetite crystals are red, magnetosome membrane vesicles are yellow, and the cellular envelope inner and outer membranes are depicted in blue. MamK filaments are green.
Source (natural)Organism: Magnetospirillum gryphiswaldense MSR-1 (magnetotactic)

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Supramolecule #2: PopZ

SupramoleculeName: PopZ / type: organelle_or_cellular_component / ID: 2 / Parent: 1
Details: 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 ...Details: 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 Magnetospirillum gryphiswaldense delta-popZ strain (lacking the endogenous popZ gene) PopZ overproduction was achieved via genomic insertion of a Tn5-Ptet-based popZ overexpression cassette.
Source (natural)Organism: Magnetospirillum gryphiswaldense MSR-1 (magnetotactic)

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Supramolecule #3: Magnetosomes

SupramoleculeName: Magnetosomes / type: organelle_or_cellular_component / ID: 3 / Parent: 1
Details: Magnetosomes are membranous organelles containing nanometer-sized crystals of magnetite present in magnetotactic bacteria.
Source (natural)Organism: Magnetospirillum gryphiswaldense MSR-1 (magnetotactic)

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Supramolecule #4: magnetite crystals

SupramoleculeName: magnetite crystals / type: organelle_or_cellular_component / ID: 4 / Parent: 3
Source (natural)Organism: Magnetospirillum gryphiswaldense MSR-1 (magnetotactic)

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Supramolecule #5: magnetosome membrane vesicles

SupramoleculeName: magnetosome membrane vesicles / type: organelle_or_cellular_component / ID: 5 / Parent: 3
Source (natural)Organism: Magnetospirillum gryphiswaldense MSR-1 (magnetotactic)

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Supramolecule #6: MamK

SupramoleculeName: MamK / type: organelle_or_cellular_component / ID: 6 / Parent: 1
Details: The filament-forming bacterial actin MamK found in magnetotactic bacteria is important for organizing magnetosome organelles into chains that are used for navigation along geomagnetic field lines.
Source (natural)Organism: Magnetospirillum gryphiswaldense MSR-1 (magnetotactic)

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Supramolecule #7: Cellular envelope

SupramoleculeName: Cellular envelope / type: organelle_or_cellular_component / ID: 7 / Parent: 1 / Details: inner and outer membranes
Source (natural)Organism: Magnetospirillum gryphiswaldense MSR-1 (magnetotactic)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7 / Details: modified flask standard medium (FSM)
GridModel: Quantifoil / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE
Details: 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..
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Sigma-Aldrich / Diameter: 15 nm

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.5 e/Å2
Details: The cumulative electron dose during the tilt series was kept below 150 e- A-2.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 5.0 µm
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 121

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