[English] 日本語
Yorodumi
- EMDB-55454: Cryo-electron tomogram of cyanobacterium Anabaena sp. PCC 7120 wi... -

+
Open data


ID or keywords:

Loading...

-
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: Benjamin L Springstein / Manjunath G Javoor / Daniela Megrian / Roman Hajdu / Dustin M Hanke / Bettina Zens / Gregor L Weiss / Florian K M Schur / Martin Loose /
Abstract: Bacteria, like eukaryotes, use conserved cytoskeletal systems for intracellular organization. The plasmid-encoded ParMRC system forms actin-like filaments that segregate low-copy number plasmids. In ...Bacteria, like eukaryotes, use conserved cytoskeletal systems for intracellular organization. The plasmid-encoded ParMRC system forms actin-like filaments that segregate low-copy number plasmids. In multicellular cyanobacteria such as sp., we found that a chromosomally encoded ParMR system has evolved into a cytoskeletal system named CorMR with a function in cell shape control rather than DNA segregation. Live-cell imaging, in vitro reconstitution, and cryo-electron microscopy revealed that CorM formed dynamically unstable, antiparallel double-stranded filaments that were recruited to the membrane by CorR through an amphipathic helix conserved in multicellular cyanobacteria. CorMR filaments were regulated by MinC, which excluded them from the poles and division plane. Comparative genomics indicated that the repurposing of ParMR and Min systems coevolved with cyanobacterial multicellularity, highlighting the evolutionary plasticity of cytoskeletal systems in bacteria.
History
DepositionOct 22, 2025-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 29, 2026-
Current statusApr 29, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_55454.png

Downloads & links

-
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 °

-
Supplemental data

-
Sample components

-
Entire : Cyanobacterium Anabaena sp. PCC 7120

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

-
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)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

-
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.

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more