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- EMDB-54060: Cryo-EM structure of the CorM filament in the presence of CorR fr... -

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Basic information

Entry
Database: EMDB / ID: EMD-54060
TitleCryo-EM structure of the CorM filament in the presence of CorR from cyanobacterium Anabaena sp. PCC 7120
Map dataSharpened map of CorM filament in the presence of CorR
Sample
  • Complex: CorM filament in the presence of CorR from cyanobacterium Anabaena sp. PCC 7120
    • Protein or peptide: CorM
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsCell shape / cytoskeleton / STRUCTURAL PROTEIN
Biological speciesNostoc sp. PCC 7120 = FACHB-418 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.92 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

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Structure visualization

Supplemental images

emd_54060.png

Downloads & links

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Map

FileDownload / File: emd_54060.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of CorM filament in the presence of CorR
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 512 pix.
= 476.928 Å		0.93 Å/pix.
x 512 pix.
= 476.928 Å		0.93 Å/pix.
x 512 pix.
= 476.928 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9315 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.128
Minimum - Maximum-0.23908794 - 0.5144387
Average (Standard dev.)0.00007009733 (±0.0154965315)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 476.928 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54060_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Non-sharpened full map of CorM filament in the presence of CorR

Fileemd_54060_additional_1.map
AnnotationNon-sharpened full map of CorM filament in the presence of CorR
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of CorM filament in the presence of CorR

Fileemd_54060_half_map_1.map
AnnotationHalf map of CorM filament in the presence of CorR
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of CorM filament in the presence of CorR

Fileemd_54060_half_map_2.map
AnnotationHalf map of CorM filament in the presence of CorR
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CorM filament in the presence of CorR from cyanobacterium Anabaen...

EntireName: CorM filament in the presence of CorR from cyanobacterium Anabaena sp. PCC 7120
Components
  • Complex: CorM filament in the presence of CorR from cyanobacterium Anabaena sp. PCC 7120
    • Protein or peptide: CorM
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: CorM filament in the presence of CorR from cyanobacterium Anabaen...

SupramoleculeName: CorM filament in the presence of CorR from cyanobacterium Anabaena sp. PCC 7120
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)

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Macromolecule #1: CorM

MacromoleculeName: CorM / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
Molecular weightTheoretical: 41.379738 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTDQPSAATP MNAAAIPLNR VSASTPINAA PANNKPNNGS SKSILSVDLG RTSTKTCVGR EPNNVVFVPA NVKQMSIEQV RGGVFEARA TDPLMDLWLE YQGKGYAVGQ LAADFGANLG VGQSKVEDAL IKVLASAGYF KLKDEISVVL GLPFLSLEQF E REKAQLTS ...String:
MTDQPSAATP MNAAAIPLNR VSASTPINAA PANNKPNNGS SKSILSVDLG RTSTKTCVGR EPNNVVFVPA NVKQMSIEQV RGGVFEARA TDPLMDLWLE YQGKGYAVGQ LAADFGANLG VGQSKVEDAL IKVLASAGYF KLKDEISVVL GLPFLSLEQF E REKAQLTS QVTGPHVLNF RGESVSLNIT KVWVMPEGYG SLLWSEAQPK KGGASPDFTK ISTAIVDIGH QTIDLLMVDN FR FARGASK SEDFGMNKFY ELVAAEIDGA DSQSLALISA VNKPKGERFY RPKGASKPTN LDDSLPNLIE QFSREICSRV LAW LPERVT DVIITGGGGE FFWEDVQRLL KDAQISAHLA APSRQANALG QYIYGEAQLS SNRAARA

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Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 6 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.4 / Details: 25mM HEPES, 150mM KCl, 1mM MgCl2, 2mM ATP
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Details: The grids were glow discharged for 60s with 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.

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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: 2236 / Average electron dose: 40.0 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

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Image processing

Details4096x4096 px movies in EER format
Particle selectionNumber selected: 424676
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: 22 / Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.92 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4) / Number images used: 124109
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: 100 / Avg.num./class: 4240 / Software - Name: cryoSPARC (ver. 4.4) / Details: 22 good classes were used out of 100 classes
FSC plot (resolution estimation)

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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
Output model

PDB-9rmi:
Cryo-EM structure of the CorM filament in the presence of CorR from cyanobacterium Anabaena sp. PCC 7120

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