|Entry||Database: EMDB / ID: EMD-9757|
|Title||Whole structure of a 15-stranded ParM filament from Clostridium botulinum|
|Sample||ParM filament coded on pCBH plasmid from Clostridium botulinum|
|Function / homology||Actin-like protein, N-terminal / ParM-like / Actin like proteins N terminal domain / Uncharacterized protein|
Function and homology information
|Biological species||Clostridium botulinum F str. 230613 (bacteria) / Clostridium botulinum Prevot_594 (bacteria)|
|Method||helical reconstruction / cryo EM / Resolution: 4.7 Å|
|Authors||Koh F / Narita A / Lee LJ / Tan YZ / Dandey VP / Tanaka K / Popp D / Robinson RC|
|Citation||Journal: Nat Commun / Year: 2019|
Title: The structure of a 15-stranded actin-like filament from Clostridium botulinum.
Authors: Fujiet Koh / Akihiro Narita / Lin Jie Lee / Kotaro Tanaka / Yong Zi Tan / Venkata P Dandey / David Popp / Robert C Robinson /
Abstract: Microfilaments (actin) and microtubules represent the extremes in eukaryotic cytoskeleton cross-sectional dimensions, raising the question of whether filament architectures are limited by protein ...Microfilaments (actin) and microtubules represent the extremes in eukaryotic cytoskeleton cross-sectional dimensions, raising the question of whether filament architectures are limited by protein fold. Here, we report the cryoelectron microscopy structure of a complex filament formed from 15 protofilaments of an actin-like protein. This actin-like ParM is encoded on the large pCBH Clostridium botulinum plasmid. In cross-section, the ~26 nm diameter filament comprises a central helical protofilament surrounded by intermediate and outer layers of six and eight twisted protofilaments, respectively. Alternating polarity of the layers allows for similar lateral contacts between each layer. This filament design is stiffer than the actin filament, and has likely been selected for during evolution to move large cargos. The comparable sizes of microtubule and pCBH ParM filaments indicate that larger filament architectures are not limited by the protomer fold. Instead, function appears to have been the evolutionary driving force to produce broad, complex filaments.
|Validation Report||PDB-ID: 6izr|
SummaryFull reportAbout validation report
|Date||Deposition: Dec 20, 2018 / Header (metadata) release: Jun 19, 2019 / Map release: Jun 19, 2019 / Update: Jul 10, 2019|
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_9757.map.gz / Format: CCP4 / Size: 35.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.331 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire ParM filament coded on pCBH plasmid from Clostridium botulinum
|Entire||Name: ParM filament coded on pCBH plasmid from Clostridium botulinum|
Number of components: 4
-Component #1: protein, ParM filament coded on pCBH plasmid from Clostridium bot...
|Protein||Name: ParM filament coded on pCBH plasmid from Clostridium botulinum|
Recombinant expression: No
|Source||Species: Clostridium botulinum F str. 230613 (bacteria)|
|Source (engineered)||Expression System: Escherichia coli BL21(DE3) (bacteria) / Vector: pET-21d|
|Source (natural)||Organelle: pCBH plasmid|
-Component #2: protein, Putative plasmid segregation protein ParM
|Protein||Name: Putative plasmid segregation protein ParM / Number of Copies: 30 / Recombinant expression: No|
|Mass||Theoretical: 39.560168 kDa|
|Source||Species: Clostridium botulinum Prevot_594 (bacteria)|
|Source (engineered)||Expression System: Escherichia coli (E. coli)|
-Component #3: ligand, ADENOSINE-5'-DIPHOSPHATE
|Ligand||Name: ADENOSINE-5'-DIPHOSPHATE / Number of Copies: 30 / Recombinant expression: No|
|Mass||Theoretical: 0.427201 kDa|
-Component #4: ligand, MAGNESIUM ION
|Ligand||Name: MAGNESIUM ION / Number of Copies: 30 / Recombinant expression: No|
|Mass||Theoretical: 2.430505 MDa|
|Specimen||Specimen state: Filament / Method: cryo EM|
|Helical parameters||Axial symmetry: C1 (asymmetric) / Delta z: 50.26 Å / Delta phi: -50.37 %deg;|
|Sample solution||Specimen conc.: 0.8 mg/mL / pH: 7.4|
|Vitrification||Cryogen name: ETHANE|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 30 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: OTHER|
|Camera||Detector: GATAN K2 SUMMIT (4k x 4k)|
|Processing||Method: helical reconstruction|
|3D reconstruction||Software: RELION / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF|
|FSC plot (resolution estimation)|
-Atomic model buiding
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