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- EMDB-37996: ParM present of genome of Desufitobacterium hafniense - Dc-cParM1 -

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Basic information

Entry
Database: EMDB / ID: EMD-37996
TitleParM present of genome of Desufitobacterium hafniense - Dc-cParM1
Map data
Sample
  • Organelle or cellular component: Dh-cParM1
    • Protein or peptide: ParM present of genome of Desufitobacterium hafniense - Dh-cParM1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsParM / genome / segregation / plasmid / STRUCTURAL PROTEIN
Function / homology: / Archaeal actin homologue MreB-like, C-terminal / Actin-like protein, N-terminal / Actin like proteins N terminal domain / ATPase, nucleotide binding domain / Uncharacterized protein
Function and homology information
Biological speciesDesulfitobacterium hafniense Y51 (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsAli S / Robinson RC / Narita A
Funding support Japan, 3 items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJCR19S5 Japan
Japan Society for the Promotion of Science (JSPS)18H02410 Japan
Japan Society for the Promotion of Science (JSPS)21H02440 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
DepositionNov 7, 2023-
Header (metadata) releaseNov 13, 2024-
Map releaseNov 13, 2024-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37996.png

Downloads & links

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Map

FileDownload / File: emd_37996.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 320 pix.
= 352. Å		1.1 Å/pix.
x 320 pix.
= 352. Å		1.1 Å/pix.
x 320 pix.
= 352. Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.024
Minimum - Maximum-0.07135027 - 0.15528093
Average (Standard dev.)-0.000016924738 (±0.0062450753)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 352.0001 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_37996_additional_1.map
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Half map: #2

Fileemd_37996_half_map_1.map
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Half map: #1

Fileemd_37996_half_map_2.map
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Sample components

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Entire : Dh-cParM1

EntireName: Dh-cParM1
Components
  • Organelle or cellular component: Dh-cParM1
    • Protein or peptide: ParM present of genome of Desufitobacterium hafniense - Dh-cParM1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Dh-cParM1

SupramoleculeName: Dh-cParM1 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: ParM present of genome of Desufitobacterium hafniense - Dh-cParM1
Source (natural)Organism: Desulfitobacterium hafniense Y51 (bacteria)
Molecular weightTheoretical: 0.405 kDa/nm

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Macromolecule #1: ParM present of genome of Desufitobacterium hafniense - Dh-cParM1

MacromoleculeName: ParM present of genome of Desufitobacterium hafniense - Dh-cParM1
type: protein_or_peptide / ID: 1
Details: genome encode ParM1 from Desulfitobacterium species
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Desulfitobacterium hafniense Y51 (bacteria)
Molecular weightTheoretical: 40.592141 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MFENDILVAG GDPGFGAIKL DAGDTKVLFP AVICKGNERI FSALGNGNVS RGTDEEMQTG SLDVIVTNHS TGVSRHYFMG SLAESLNPN EAHYCWDEDK STDEEATALL VVALAVAQKE PKANIYLGTG VPVKYYAALK DKYEAELKGT WSVAFRSGPF K GQTRQLTI ...String:
MFENDILVAG GDPGFGAIKL DAGDTKVLFP AVICKGNERI FSALGNGNVS RGTDEEMQTG SLDVIVTNHS TGVSRHYFMG SLAESLNPN EAHYCWDEDK STDEEATALL VVALAVAQKE PKANIYLGTG VPVKYYAALK DKYEAELKGT WSVAFRSGPF K GQTRQLTI IRSRVLPQSY GVFIKETLNE YGIPISPKLF NGYVVVIDPG FRTTDVATFY DGVMLDPPNS FSIEKGLKWA YT GVAEQLK EMTINHANPI ETDDKELDKV FRVNEGMYPW NNGAINLNPV MQDMLGQLGT DISREVKKSL KPMLGKIHTV LVA GKVGEM IFEHLQFENK VLIENPQFGN ATGFRIMAAN LVNNITKKAN AAP

UniProtKB: Uncharacterized protein

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Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 1 / 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

Concentration10.0 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: MOLYBDENUM / Mesh: 200 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 K / Instrument: LEICA EM GP
DetailsParM present of genome of Desufitobacterium hafniense - Dc-cParM1

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber classes used: 2
Applied symmetry - Helical parameters - Δz: 24.5 Å
Applied symmetry - Helical parameters - Δ&Phi: 156.03 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1/4.0)
Software - details: 3D structure was reconstructed using RELION software
Number images used: 2100
CTF correctionSoftware - Name: RELION (ver. 3.1/4.0)
Software - details: Gctf incorporated RELION was used for CFT determination and correction
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Segment selectionNumber selected: 2500
Startup modelType of model: OTHER / Details: Model reconstructed from negative stained images
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
DetailsInitial fitting was performed using chimera and MDFF performed by ISOLDE and final real space refine by Phenix real space refinement.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8x1i:
ParM present of genome of Desufitobacterium hafniense - Dh-cParM1

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