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- EMDB-9757: pCBH ParM filament -

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Basic information

Entry
Database: EMDB / ID: EMD-9757
TitlepCBH ParM filament
Map dataWhole map of a ParM filament from pCBH of Clostridium botulinum
Sample
  • Complex: ParM filament coded on pCBH plasmid from Clostridium botulinum
    • Protein or peptide: Putative plasmid segregation protein ParM
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsParM / filaments / cytoskeleton / PROTEIN FIBRIL
Function / homologyActin-like protein, N-terminal / Actin like proteins N terminal domain / ParM-like / ATPase, nucleotide binding domain / Actin-like protein N-terminal domain-containing protein
Function and homology information
Biological speciesClostridium botulinum F str. 230613 (bacteria) / Clostridium botulinum Prevot_594 (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 4.7 Å
AuthorsKoh F / Narita A
Funding support United States, 3 items
OrganizationGrant numberCountry
Other privateSF349247 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103310 United States
Other privateF00316 United States
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.
History
DepositionDec 20, 2018-
Header (metadata) releaseJun 19, 2019-
Map releaseJun 19, 2019-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.038
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.038
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6izr
  • Surface level: 0.038
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6izr
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9757.png

Downloads & links

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Map

FileDownload / File: emd_9757.map.gz / Format: CCP4 / Size: 35.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationWhole map of a ParM filament from pCBH of Clostridium botulinum
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.33 Å/pix.
x 210 pix.
= 279.51 Å		1.33 Å/pix.
x 210 pix.
= 279.51 Å		1.33 Å/pix.
x 210 pix.
= 279.51 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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.038 / Movie #1: 0.038
Minimum - Maximum-0.058636397 - 0.14474924
Average (Standard dev.)0.0072660567 (±0.015892716)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions210210210
Spacing210210210
CellA=B=C: 279.50998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3311.3311.331
M x/y/z210210210
origin x/y/z0.0000.0000.000
length x/y/z279.510279.510279.510
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ480480480
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS210210210
D min/max/mean-0.0590.1450.007

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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
Components
  • Complex: ParM filament coded on pCBH plasmid from Clostridium botulinum
    • Protein or peptide: Putative plasmid segregation protein ParM
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: ParM filament coded on pCBH plasmid from Clostridium botulinum

SupramoleculeName: ParM filament coded on pCBH plasmid from Clostridium botulinum
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Clostridium botulinum F str. 230613 (bacteria) / Organelle: pCBH plasmid

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Macromolecule #1: Putative plasmid segregation protein ParM

MacromoleculeName: Putative plasmid segregation protein ParM / type: protein_or_peptide / ID: 1 / Number of copies: 30 / Enantiomer: LEVO
Source (natural)Organism: Clostridium botulinum Prevot_594 (bacteria)
Molecular weightTheoretical: 39.560168 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNKYTIAIDL GYGQIKGINQ DNKRVIFPSI ISSGKDRSLD TFFNSIDNIV DNIHVKILDE YFNEKEYFVG ELAKRQPSNS SFINRDNKI NSEENKVLLA TALGLLIPND LPNDTKIHIV TGLPLEHFIK QKQALNDMLK DFEHTIKFVD HNFSRNIKFE E SNITLFPQ ...String:
MNKYTIAIDL GYGQIKGINQ DNKRVIFPSI ISSGKDRSLD TFFNSIDNIV DNIHVKILDE YFNEKEYFVG ELAKRQPSNS SFINRDNKI NSEENKVLLA TALGLLIPND LPNDTKIHIV TGLPLEHFIK QKQALNDMLK DFEHTIKFVD HNFSRNIKFE E SNITLFPQ GAGAIFSKIN NDISSLLIKE TFIGLIDVGF KTTDIVVFRI NKDKEPVFEQ EMSATLDGLG MINIYNTMDK AF TDNSRDG SKLNTEQLML LCEEGKIFFK GDYIDLKKDL IKARKTLSTN IINKADGLWG SRKNSFNSIM IAGGGGKVLY NHL KLIEPN MCQLIDNPEF ANAIGYLEFG KQF

UniProtKB: Actin-like protein N-terminal domain-containing protein

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Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 30 / 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: 30 / 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

Concentration0.8 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: MOLYBDENUM / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 50.26 Å
Applied symmetry - Helical parameters - Δ&Phi: -50.37 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 33356
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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