[English] 日本語
Yorodumi
- EMDB-54062: Cryo-EM structure of the delta1-40 CorM filament from cyanobacter... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-54062
TitleCryo-EM structure of the delta1-40 CorM filament from cyanobacterium Anabaena sp. PCC 7120
Map dataSharpened full map map of delta1-40 CorM filament
Sample
  • Complex: delta1-40 CorM filament from cyanobacterium Anabaena sp. PCC 7120
    • Protein or peptide: CorM
KeywordsCell shape / Cytoskeleton / STRUCTURAL PROTEIN
Biological speciesNostoc sp. PCC 7120 = FACHB-418 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.42 Å
AuthorsSpringstein BL / Javoor MG / Megrian D / Hajdu R / Hanke DM / 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
DepositionJun 18, 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_54062.png

Downloads & links

-
Map

FileDownload / File: emd_54062.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened full map map of delta1-40 CorM filament
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 512 pix.
= 489.011 Å		0.96 Å/pix.
x 512 pix.
= 489.011 Å		0.96 Å/pix.
x 512 pix.
= 489.011 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9551 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0838
Minimum - Maximum-0.12231709 - 0.35332263
Average (Standard dev.)-0.00017321469 (±0.013003625)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 489.0112 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_54062_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Non-sharpened full map of delta1-40 CorM filament

Fileemd_54062_additional_1.map
AnnotationNon-sharpened full map of delta1-40 CorM filament
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map of delta1-40 CorM filament

Fileemd_54062_half_map_1.map
AnnotationHalf map of delta1-40 CorM filament
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map of delta1-40 CorM filament

Fileemd_54062_half_map_2.map
AnnotationHalf map of delta1-40 CorM filament
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : delta1-40 CorM filament from cyanobacterium Anabaena sp. PCC 7120

EntireName: delta1-40 CorM filament from cyanobacterium Anabaena sp. PCC 7120
Components
  • Complex: delta1-40 CorM filament from cyanobacterium Anabaena sp. PCC 7120
    • Protein or peptide: CorM

-
Supramolecule #1: delta1-40 CorM filament from cyanobacterium Anabaena sp. PCC 7120

SupramoleculeName: delta1-40 CorM filament from cyanobacterium Anabaena sp. PCC 7120
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)

-
Macromolecule #1: CorM

MacromoleculeName: CorM / type: protein_or_peptide / ID: 1
Details: Delta1-40 mutant of CorM, missing the first 40 amino acid residues.
Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: SKSILSVDLG RTSTKTCVGR EPNNVVFVPA NVKQMSIEQV RGGVFEARAT DPLMDLWLEY QGKGYAVGQL AADFGANLGV GQSKVEDALI KVLASAGYFK LKDEISVVLG LPFLSLEQFE REKAQLTSQV TGPHVLNFRG ESVSLNITKV WVMPEGYGSL LWSEAQPKKG ...String:
SKSILSVDLG RTSTKTCVGR EPNNVVFVPA NVKQMSIEQV RGGVFEARAT DPLMDLWLEY QGKGYAVGQL AADFGANLGV GQSKVEDALI KVLASAGYFK LKDEISVVLG LPFLSLEQFE REKAQLTSQV TGPHVLNFRG ESVSLNITKV WVMPEGYGSL LWSEAQPKKG GASPDFTKIS TAIVDIGHQT IDLLMVDNFR FARGASKSED FGMNKFYELV AAEIDGADSQ SLALISAVNK PKGERFYRPK GASKPTNLDD SLPNLIEQFS REICSRVLAW LPERVTDVII TGGGGEFFWE DVQRLLKDAQ ISAHLAAPSR QANALGQYIY GEAQLSSNRA ARA

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

-
Sample preparation

BufferpH: 7.4 / Details: 25mM HEPES, 150mM KCl, 1mM MgCl2, 2mM ATP
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Details: Grids were glow discharged for 60s at 25mA.
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 298.15 K / Instrument: LEICA EM GP
Details: Vitrification was carried out after 3-3.5s of blotting.

-
Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 3162 / Average electron dose: 60.0 e/Å2 / Details: The movies were collected in EER mode
Electron beamAcceleration voltage: 200 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: 0.9 µm / Nominal magnification: 150000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

+
Image processing

Details4096x4096 px movies in EER format
Particle selectionNumber selected: 831156
Details: Filament tracer in cryoSPARC was used for particle picking
CTF correctionSoftware - Name: cryoSPARC (ver. 4.4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Details: No initial model was used. Ab-initio model was generated in cryoSPARC
Final reconstructionNumber classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.42 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4) / Number images used: 127289
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4) / Details: Ab-initio model generation in cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4) / Details: Refinement in cryoSPARC
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 4.4)
Details: 1 good class with 127289 particles was used out of 3 classes
FSC plot (resolution estimation)

+
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