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- EMDB-9758: Averaged strand structure of a 15-stranded ParM filament from Clo... -

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Entry
Database: EMDB / ID: EMD-9758
TitleAveraged strand structure of a 15-stranded ParM filament from Clostridium botulinum
Map data
SampleParM filament coded on pCBH plasmid from Clostridium botulinum
  • Putative plasmid segregation protein ParM
  • (ligand) x 2
Function / homologyActin-like protein, N-terminal / ParM-like / Actin like proteins N terminal domain / Uncharacterized protein
Function and homology information
Biological speciesClostridium botulinum F str. 230613 (bacteria) / Clostridium botulinum Prevot_594 (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsKoh F / Narita A / Lee LJ / Tan YZ / Dandey VP / Tanaka K / Popp D / Robinson RC
CitationJournal: 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 ReportPDB-ID: 6izv

SummaryFull reportAbout validation report
DateDeposition: Dec 20, 2018 / Header (metadata) release: Jun 19, 2019 / Map release: Jun 19, 2019 / Update: Jul 10, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.191
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.191
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6izv
  • Surface level: 0.191
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_9758.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.33 Å/pix.
x 100 pix.
= 133.1 Å
1.33 Å/pix.
x 100 pix.
= 133.1 Å
1.33 Å/pix.
x 100 pix.
= 133.1 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.331 Å
Density
Contour LevelBy AUTHOR: 0.191 / Movie #1: 0.191
Minimum - Maximum-0.4516051 - 1.0867001
Average (Standard dev.)0.010632155 (±0.07728419)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 133.09999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3311.3311.331
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z133.100133.100133.100
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ480480480
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
D min/max/mean-0.4521.0870.011

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Supplemental data

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Sample components

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Entire ParM filament coded on pCBH plasmid from Clostridium botulinum

EntireName: ParM filament coded on pCBH plasmid from Clostridium botulinum
Number of components: 4

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Component #1: protein, ParM filament coded on pCBH plasmid from Clostridium bot...

ProteinName: ParM filament coded on pCBH plasmid from Clostridium botulinum
Recombinant expression: No
SourceSpecies: Clostridium botulinum F str. 230613 (bacteria)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria) / Vector: pET-21d
Source (natural)Organelle: pCBH plasmid

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Component #2: protein, Putative plasmid segregation protein ParM

ProteinName: Putative plasmid segregation protein ParM / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 39.560168 kDa
SourceSpecies: Clostridium botulinum Prevot_594 (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: ligand, ADENOSINE-5'-DIPHOSPHATE

LigandName: ADENOSINE-5'-DIPHOSPHATE / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.427201 kDa

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Component #4: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Filament / Method: cryo EM
Helical parametersAxial symmetry: C1 (asymmetric) / Delta z: 50.26 Å / Delta phi: -50.37 %deg;
Sample solutionSpecimen conc.: 0.8 mg/mL / pH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 30 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: helical reconstruction
3D reconstructionSoftware: RELION / Resolution: 4.2 Å / Resolution method: OTHER

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Atomic model buiding

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