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

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Basic information

Entry
Database: EMDB / ID: EMD-9758
TitleAveraged strand structure of a 15-stranded ParM filament from Clostridium botulinum
Map dataAveraged density map for the medium layer of pCBH ParM filament
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
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: 4.2 Å
AuthorsKoh F / Narita A / Lee LJ / Tan YZ / Dandey VP / Tanaka K / Popp D / Robinson RC
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-
UpdateMar 23, 2022-
Current statusMar 23, 2022Processing site: PDBj / Status: Released

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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)
AnnotationAveraged density map for the medium layer of pCBH ParM filament
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
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
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria) / Recombinant plasmid: pET-21d

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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: 2 / 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

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Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 2 / 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
VitrificationCryogen name: ETHANE

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Electron microscopy

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

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Image processing

Final angle assignmentType: NOT APPLICABLE
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: 4.2 Å / Resolution method: OTHER / Software - Name: RELION (ver. 2.1) / Number images used: 33356

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