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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: Springstein BL / Javoor MG / Megrian D / Hajdu R / Hanke DM / Schur FKM / Loose M
History
DepositionJun 18, 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_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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