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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 / ParM-like / 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: To Be Published
Title: Bacterial genome encoded ParMs
Authors: Ali S / Robinson RC / Narita A
History
DepositionNov 7, 2023-
Header (metadata) releaseNov 13, 2024-
Map releaseNov 13, 2024-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing 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

Size
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Others
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

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

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
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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