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- EMDB-33007: A CBg-ParM filament with ADP -

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Basic information

Entry
Database: EMDB / ID: EMD-33007
TitleA CBg-ParM filament with ADP
Map dataCBg-ParM filament with ADP
Sample
  • Complex: CBg-ParM filament with ADP
    • Protein or peptide: ParM/StbA family protein
  • Ligand: ADENOSINE-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: 3.9 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: To Be Published
Title: A new actin-like filament from Clostridium botulinum exhibits a new system of filament turn over
Authors: Koh A / Ali S / Popp D / Tanaka K / Kitaoku Y / Miyazaki N / Iwasaki K / Mitsuoka K / Robert R / Narita A
History
DepositionMar 4, 2022-
Header (metadata) releaseMar 8, 2023-
Map releaseMar 8, 2023-
UpdateJun 26, 2024-
Current statusJun 26, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33007.png

Downloads & links

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Map

FileDownload / File: emd_33007.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCBg-ParM filament with ADP
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 384 pix.
= 334.08 Å		0.87 Å/pix.
x 384 pix.
= 334.08 Å		0.87 Å/pix.
x 384 pix.
= 334.08 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: 0.016
Minimum - Maximum-0.04994001 - 0.109655544
Average (Standard dev.)0.000086486405 (±0.0018449463)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 334.08002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_33007_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_33007_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CBg-ParM filament with ADP

EntireName: CBg-ParM filament with ADP
Components
  • Complex: CBg-ParM filament with ADP
    • Protein or peptide: ParM/StbA family protein
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: CBg-ParM filament with ADP

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

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Macromolecule #1: ParM/StbA family protein

MacromoleculeName: ParM/StbA family protein / 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: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 5 / 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: 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 mMATPadenosine triphosphate
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 II (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: 23.3 Å
Applied symmetry - Helical parameters - Δ&Phi: 167.6 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 36762
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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