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- EMDB-50515: PomX filament from Myxococcus xanthus -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-50515
TitlePomX filament from Myxococcus xanthus
Map data
Sample
  • Complex: filaments of PomX
Keywordsprokaryotes / intermediate filaments / PROTEIN FIBRIL
Biological speciesMyxococcus xanthus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.0 Å
AuthorsXu P / Schumacher D / Liu C / Dickmanns M / Beck F / Plitzko J / Baumeister W / Sogaard-Andersen L
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: To Be Published
Title: PomX filament from Myxococcus xanthus
Authors: Xu P / Schumacher D / Liu C / Dickmanns M / Beck F / Plitzko J / Baumeister W / Sogaard-Andersen L
History
DepositionMay 31, 2024-
Header (metadata) releaseJun 26, 2024-
Map releaseJun 26, 2024-
UpdateJun 26, 2024-
Current statusJun 26, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50515.png

Downloads & links

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Map

FileDownload / File: emd_50515.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.18 Å/pix.
x 200 pix.
= 436. Å		2.18 Å/pix.
x 200 pix.
= 436. Å		2.18 Å/pix.
x 200 pix.
= 436. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.18 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.83
Minimum - Maximum-1.4294245 - 3.3007042
Average (Standard dev.)0.007262861 (±0.089402586)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 436.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50515_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_50515_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_50515_half_map_2.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 : filaments of PomX

EntireName: filaments of PomX
Components
  • Complex: filaments of PomX

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Supramolecule #1: filaments of PomX

SupramoleculeName: filaments of PomX / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Myxococcus xanthus (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4 / Details: 20mM Tris/HCl; 200mM NaCl; 1mM EDTA; pH 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV
DetailsTo purify PomX-His6 plasmid pEMR3 was propagated in E. coli(DE3) cells (NEB). Cells were grown in LB medium with kanamycin at 30 degree to an OD600 of 0.6. Protein accumulation was induced with 0.5mM IPTG for 16 hrs at 18 degree.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 17653 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2150525 / Details: template free filament tracing from cryoSPARC
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: cryoSPARC (ver. 3.4), RELION (ver. 4.0)) / Number images used: 161664
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.4)
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC (ver. 3.4)
FSC plot (resolution estimation)

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