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- PDB-7x54: A CBg-ParM filament with ADP -

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Basic information

Entry
Database: PDB / ID: 7x54
TitleA CBg-ParM filament with ADP
ComponentsParM/StbA family protein
KeywordsCELL CYCLE / ParM actin-like plasmid segregation
Function / homologyATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta / ADENOSINE-5'-DIPHOSPHATE / :
Function and homology information
Biological speciesClostridium botulinum Bf (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.9 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: 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, 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

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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)164,98415
Polymers162,7275
Non-polymers2,25810
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 Bf (bacteria) / Gene: EXN02_10840 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A6B3ZKE5
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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 ADP / 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 triphosphateATP1
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 II (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: 167.6 ° / Axial rise/subunit: 23.3 Å / Axial symmetry: C1
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 36762 / Symmetry type: HELICAL

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