8X1I | pdb_00008x1i

ParM present of genome of Desufitobacterium hafniense - Dh-cParM1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Bacterial genome-encoded ParMs.

Ali, S.Koh, A.Popp, D.Tanaka, K.Kitaoku, Y.Miyazaki, N.Iwasaki, K.Mitsuoka, K.Robinson, R.C.Narita, A.

(2025) J Biological Chem 301: 110351-110351

  • DOI: https://doi.org/10.1016/j.jbc.2025.110351
  • Primary Citation of Related Structures:  
    7X54, 7X55, 7X56, 7X59, 8X1I

  • PubMed 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 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.


  • Organizational Affiliation
    • Research Institute for Interdisciplinary Science, Okayama University, Okayama, Japan; Institute of Molecular and Cell Biology, A∗STAR (Agency for Science, Technology and Research), Biopolis, Singapore.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ParM present of genome of Desufitobacterium hafniense - Dh-cParM1A [auth B]369Desulfitobacterium hafniense Y51Mutation(s): 0 
Gene Names: DSY2109
UniProt
Find proteins for Q24VP4 (Desulfitobacterium hafniense (strain Y51))
Explore Q24VP4 
Go to UniProtKB:  Q24VP4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ24VP4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTISOLDE
RECONSTRUCTIONRELION3.1/4.0

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Science and TechnologyJapanJPMJCR19S5
Japan Society for the Promotion of Science (JSPS)Japan18H02410
Japan Society for the Promotion of Science (JSPS)Japan21H02440

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-13
    Type: Initial release
  • Version 1.1: 2025-07-16
    Changes: Data collection, Database references