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- PDB-7x59: A Cbc-ParM filament with GTP or GDPPi -

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Basic information

Entry
Database: PDB / ID: 7x59
TitleA Cbc-ParM filament with GTP or GDPPi
ComponentsParM/StbA family protein
KeywordsCELL CYCLE / ParM actin-like plasmid segregation
Function / homologyGUANOSINE-5'-TRIPHOSPHATE / :
Function and homology information
Biological speciesClostridium botulinum (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 6.5 Å
AuthorsKoh, A. / Ali, S. / Robinson, R. / Narita, A.
Funding support Japan, 3items
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, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update
Revision 1.2Jul 16, 2025Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_entry_details / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update / _em_admin.title / _pdbx_entry_details.has_protein_modification / _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ParM/StbA family protein
B: ParM/StbA family protein
C: ParM/StbA family protein
D: ParM/StbA family protein
E: ParM/StbA family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,34310
Polymers162,7275
Non-polymers2,6165
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
ParM/StbA family protein


Mass: 32545.352 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: EXN02_10840 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A6B3ZKE5
#2: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, 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: helical reconstruction

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Sample preparation

ComponentName: CBg-ParM filament with GTP or GDPPi / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Clostridium botulinum (bacteria) / Strain: Bf
Source (recombinant)Organism: Escherichia coli BL21 (bacteria) / Strain: BL21
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMpotassium chlorideKCl1
220 mMHEPES-HClHEPES-HCl1
33 mMadenosine triphosphateGTP1
SpecimenConc.: 0.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 45 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameVersionCategory
11RELION3.1final Euler assignment
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 165.7 ° / Axial rise/subunit: 22.6 Å / Axial symmetry: C1
3D reconstructionResolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 70754 / Symmetry type: HELICAL

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