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- EMDB-55454: Cryo-electron tomogram of cyanobacterium Anabaena sp. PCC 7120 wi... -

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Basic information

Entry
Database: EMDB / ID: EMD-55454
TitleCryo-electron tomogram of cyanobacterium Anabaena sp. PCC 7120 with putative CorM filaments (Isonet-processed)
Map dataCryo-electron tomogram (8x binned) of cyanobacterium Anabaena sp. PCC 7120.
Sample
  • Cell: Cyanobacterium Anabaena sp. PCC 7120
KeywordsCell shape / cytoskeleton / STRUCTURAL PROTEIN
Biological speciesNostoc sp. PCC 7120 = FACHB-418 (bacteria)
Methodelectron tomography / cryo EM
AuthorsSpringstein BL / Javoor MG / Megrian D / Hajdu R / Hanke DM / Zens B / Weiss GL / Schur FKM / Loose M
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)ActinID 101076260European Union
CitationJournal: Science / Year: 2026
Title: Repurposing of a DNA segregation machinery into a cytoskeletal system controlling cell shape
Authors: Springstein BL / Javoor MG / Megrian D / Hajdu R / Hanke DM / Schur FKM / Loose M
History
DepositionOct 22, 2025-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55454.png

Downloads & links

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Map

FileDownload / File: emd_55454.map.gz / Format: CCP4 / Size: 350.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-electron tomogram (8x binned) of cyanobacterium Anabaena sp. PCC 7120.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
11.04 Å/pix.
x 250 pix.
= 2760. Å		11.04 Å/pix.
x 720 pix.
= 7948.8 Å		11.04 Å/pix.
x 510 pix.
= 5630.4 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 11.04 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-5.832708 - 2.813985
Average (Standard dev.)-0.47528687 (±0.35272118)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions720510250
Spacing510720250
CellA: 5630.4 Å / B: 7948.8 Å / C: 2760.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Cyanobacterium Anabaena sp. PCC 7120

EntireName: Cyanobacterium Anabaena sp. PCC 7120
Components
  • Cell: Cyanobacterium Anabaena sp. PCC 7120

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Supramolecule #1: Cyanobacterium Anabaena sp. PCC 7120

SupramoleculeName: Cyanobacterium Anabaena sp. PCC 7120 / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)

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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: 8
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 301 K / Instrument: LEICA EM GP / Details: The grids were back-side blotted..
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.03 / Focused ion beam - Duration: 2400 / Focused ion beam - Temperature: 83 K / Focused ion beam - Initial thickness: 3000 / Focused ion beam - Final thickness: 200
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is ThermoFisher Scientific Aquilos 2. This is not in a list of allowed values {'OTHER', 'DB235'} so OTHER is written into the XML file.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 41 / Average exposure time: 0.368 sec. / Average electron dose: 4.39 e/Å2
Details: The images were collected in counting mode with 8 frames per tilt.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 64000
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

Details5760x4096px
Final reconstructionAlgorithm: BACK PROJECTION / Software - Name: AreTomo (ver. AreTomo2)
Details: AreTomo2 (version 1.3.4) software was used for ctf-correction, tilt series alignment and tomogram recostruction using Weighted Back Projection method. To fill the missing-wedge information, ...Details: AreTomo2 (version 1.3.4) software was used for ctf-correction, tilt series alignment and tomogram recostruction using Weighted Back Projection method. To fill the missing-wedge information, IsoNet correction was performed.
Number images used: 41
CTF correctionSoftware - Name: AreTomo (ver. AreTomo2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Details: CorM was predicted using the AF3 server. An ADP molecule was added to the Apo-CorM molecule during fitting
RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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