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- EMDB-33009: A Cbc-ParM filament with GDP -

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Basic information

Entry
Database: EMDB / ID: EMD-33009
TitleA Cbc-ParM filament with GDP
Map data
Sample
  • Complex: CBg-ParM filament with GDP
    • Protein or peptide: Cbc-ParM
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsParM actin-like plasmid segregation / CELL CYCLE
Function / homology:
Function and homology information
Biological speciesClostridium botulinum (bacteria) / Clostridium botulinum Bf (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsKoh A / Ali S / Robinson R / Narita A
Funding support Japan, 3 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18H02410 Japan
Japan Science and TechnologyJPMJCR19S5 Japan
Japan Science and TechnologyJPMJCR19S5 Japan
CitationJournal: J Biol Chem / Year: 2025
Title: Bacterial genome-encoded ParMs.
Authors: Samson Ali / Adrian Koh / David Popp / Kotaro Tanaka / Yoshihito Kitaoku / Naoyuki Miyazaki / Kenji Iwasaki / Kaoru Mitsuoka / Robert C Robinson / Akihiro Narita /
Abstract: ParMs generally exist on low-copy number plasmids where they contribute to plasmid segregation and stable inheritance. We carried out bioinformatics analysis, which indicated that ParM genes are not ...ParMs generally exist on low-copy number plasmids where they contribute to plasmid segregation and stable inheritance. We carried out bioinformatics analysis, which indicated that ParM genes are not only confined to plasmids but are also occasionally found on genomes. Here we report the discovery and characterization of two chromosome-encoded ParMs (cParMs) from the genomes of Desulfitobacterium hafniense (Dh-cParM1) and Clostridium botulinum (Cb-cParM). Both cParMs form filaments, exhibit nucleotide hydrolysis, and possess characteristic ParM subunit structures. Dh-cParM1 forms single and tightly coupled double filaments and is highly conserved on the chromosomes of five of six Desulfitobacterium species. Interestingly, these bacteria have not been reported to harbor plasmids. Cb-cParM possesses unique properties. Its filaments were stable after nucleotide hydrolysis and Pi release, and its ParR (Cb-cParR) did not affect the initial phase of Cb-cParM polymerization but displayed properties of a depolymerization factor for mature filaments. These results indicate functional, polymerizing ParMs can be encoded on genomes, suggesting that ParM roles may extend to other functions beyond plasmid segregation.
History
DepositionMar 4, 2022-
Header (metadata) releaseMar 8, 2023-
Map releaseMar 8, 2023-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33009.png

Downloads & links

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Map

FileDownload / File: emd_33009.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 200 pix.
= 174. Å		0.87 Å/pix.
x 200 pix.
= 174. Å		0.87 Å/pix.
x 200 pix.
= 174. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.87 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.07890688 - 0.20357713
Average (Standard dev.)0.0020519989 (±0.011093054)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 174.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : CBg-ParM filament with GDP

EntireName: CBg-ParM filament with GDP
Components
  • Complex: CBg-ParM filament with GDP
    • Protein or peptide: Cbc-ParM
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: CBg-ParM filament with GDP

SupramoleculeName: CBg-ParM filament with GDP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Clostridium botulinum (bacteria) / Strain: Bf

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Macromolecule #1: Cbc-ParM

MacromoleculeName: Cbc-ParM / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Clostridium botulinum Bf (bacteria)
Molecular weightTheoretical: 32.545352 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MKITVVDLGN INVKYVGENK GRFSSKITND YQSYEEGFQR VEYNGIKTYI GVGELSREFN KADRDYMAQL LYSLAKANTA DTKEINLTL LLPIIQMKNK TRLIETLKGE NFKFKFNGID REIKINDLMV LPEGYASYYS LDIENKKGDV CILDLGSRTI N ICVLENAK ...String:
MKITVVDLGN INVKYVGENK GRFSSKITND YQSYEEGFQR VEYNGIKTYI GVGELSREFN KADRDYMAQL LYSLAKANTA DTKEINLTL LLPIIQMKNK TRLIETLKGE NFKFKFNGID REIKINDLMV LPEGYASYYS LDIENKKGDV CILDLGSRTI N ICVLENAK IVKTNTIKLG SFDFYSKIKS LENAKGEDYI EEDIQRLIDN GLIKVDSKQY IEFLSDILNA VKPYVNLKTY NT IFTGGTS LMLKEYIEKL PLNKFKVHPN ALTSNVDGAM EASKKVWN

UniProtKB: UNIPROTKB: A0A6B3ZKE5

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Macromolecule #2: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 5 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 5 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.7 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
150.0 mMKClpotassium chloride
20.0 mMHEPES-HClHEPES-HCl
3.0 mMGTPadenosine triphosphate
GridModel: Quantifoil / Material: MOLYBDENUM / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 23.2 Å
Applied symmetry - Helical parameters - Δ&Phi: 167.8 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 40599
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Conventional helical reconstruction
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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