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- PDB-9rmi: Cryo-EM structure of the CorM filament in the presence of CorR fr... -

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Basic information

Entry
Database: PDB / ID: 9rmi
TitleCryo-EM structure of the CorM filament in the presence of CorR from cyanobacterium Anabaena sp. PCC 7120
ComponentsCorM
KeywordsSTRUCTURAL PROTEIN / Cell shape / cytoskeleton
Function / homologyADENOSINE-5'-DIPHOSPHATE
Function and homology information
Biological speciesNostoc sp. PCC 7120 = FACHB-418 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.92 Å
AuthorsSpringstein, B.L. / Javoor, M.G. / Megrian, D. / Hajdu, R. / Hanke, D.M. / Schur, F.K.M. / Loose, M.
Funding supportEuropean Union, 1items
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, B.L. / Javoor, M.G. / Megrian, D. / Hajdu, R. / Hanke, D.M. / Schur, F.K.M. / Loose, M.
History
DepositionJun 18, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
G: CorM
K: CorM
C: CorM
E: CorM
I: CorM
A: CorM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)250,84212
Polymers248,2786
Non-polymers2,5636
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
CorM


Mass: 41379.738 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: CorM filament in the presence of CorR from cyanobacterium Anabaena sp. PCC 7120
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
Source (recombinant)Organism: E. coli (DE3) / Strain: C41
Buffer solutionpH: 7.4 / Details: 25mM HEPES, 150mM KCl, 1mM MgCl2, 2mM ATP
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: The grids were glow discharged for 60s with 25mA / Grid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 298.15 K
Details: Vitrification was carried out after 3-3.5s of blotting

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 150000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 900 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2236 / Details: The movies were collected in EER mode
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC4.4particle selection
2EPU3.7.0image acquisitionThermo Fisher Scientific
4cryoSPARC4.4CTF correction
7UCSF ChimeraX1.9model fitting
9cryoSPARC4.4initial Euler assignment
10cryoSPARC4.4final Euler assignment
11cryoSPARC4.4classification
12cryoSPARC4.43D reconstruction
13ISOLDEv.19model refinement
Image processingDetails: 4096x4096 px movies in EER format
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 424676
Details: Filament tracer in cryoSPARC was used for particle picking
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 124109 / Algorithm: FOURIER SPACE / Num. of class averages: 22 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingDetails: CorM was predicted using the AF3 server. An ADP molecule was added to the Apo-CorM molecule during fitting
Source name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 115.67 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003215972
ELECTRON MICROSCOPYf_angle_d0.572321654
ELECTRON MICROSCOPYf_chiral_restr0.04132406
ELECTRON MICROSCOPYf_plane_restr0.00462802
ELECTRON MICROSCOPYf_dihedral_angle_d9.42842214

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