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- EMDB-2572: Cryo-EM structure of Plasmodium falciparum actin I -

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Basic information

Entry
Database: EMDB / ID: EMD-2572
TitleCryo-EM structure of Plasmodium falciparum actin I
Map dataCryo-EM structure of Plasmodium falciparum actin I
Sample
  • Sample: Plasmodium falciparum Actin I
  • Protein or peptide: Plasmodium actin I
KeywordsPlasmodium falciparum Actin I / malaria parasite
Function / homology
Function and homology information


Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain
Similarity search - Domain/homology
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Methodsingle particle reconstruction / cryo EM / Resolution: 25.0 Å
AuthorsVahokoski J / Bhargav SP / Desfosses A / Andreadaki M / Kumpula E / Ignatev A / Martinez SM / Lepper S / Frischknecht F / Siden-Kiamos I ...Vahokoski J / Bhargav SP / Desfosses A / Andreadaki M / Kumpula E / Ignatev A / Martinez SM / Lepper S / Frischknecht F / Siden-Kiamos I / Sachse C / Kursula I
CitationJournal: PLoS Pathog / Year: 2014
Title: Structural differences explain diverse functions of Plasmodium actins.
Authors: Juha Vahokoski / Saligram Prabhakar Bhargav / Ambroise Desfosses / Maria Andreadaki / Esa-Pekka Kumpula / Silvia Muñico Martinez / Alexander Ignatev / Simone Lepper / Friedrich Frischknecht ...Authors: Juha Vahokoski / Saligram Prabhakar Bhargav / Ambroise Desfosses / Maria Andreadaki / Esa-Pekka Kumpula / Silvia Muñico Martinez / Alexander Ignatev / Simone Lepper / Friedrich Frischknecht / Inga Sidén-Kiamos / Carsten Sachse / Inari Kursula /
Abstract: Actins are highly conserved proteins and key players in central processes in all eukaryotic cells. The two actins of the malaria parasite are among the most divergent eukaryotic actins and also ...Actins are highly conserved proteins and key players in central processes in all eukaryotic cells. The two actins of the malaria parasite are among the most divergent eukaryotic actins and also differ from each other more than isoforms in any other species. Microfilaments have not been directly observed in Plasmodium and are presumed to be short and highly dynamic. We show that actin I cannot complement actin II in male gametogenesis, suggesting critical structural differences. Cryo-EM reveals that Plasmodium actin I has a unique filament structure, whereas actin II filaments resemble canonical F-actin. Both Plasmodium actins hydrolyze ATP more efficiently than α-actin, and unlike any other actin, both parasite actins rapidly form short oligomers induced by ADP. Crystal structures of both isoforms pinpoint several structural changes in the monomers causing the unique polymerization properties. Inserting the canonical D-loop to Plasmodium actin I leads to the formation of long filaments in vitro. In vivo, this chimera restores gametogenesis in parasites lacking actin II, suggesting that stable filaments are required for exflagellation. Together, these data underline the divergence of eukaryotic actins and demonstrate how structural differences in the monomers translate into filaments with different properties, implying that even eukaryotic actins have faced different evolutionary pressures and followed different paths for developing their polymerization properties.
History
DepositionFeb 10, 2014-
Header (metadata) releaseMar 12, 2014-
Map releaseApr 30, 2014-
UpdateApr 30, 2014-
Current statusApr 30, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.125
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.125
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.125
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2572-Act...

Downloads & links

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Map

FileDownload / File: emd_2572.map.gz / Format: CCP4 / Size: 917 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of Plasmodium falciparum actin I
Voxel sizeX=Y=Z: 4.412 Å
Density
Contour LevelBy AUTHOR: 0.125 / Movie #1: 0.125
Minimum - Maximum-0.36687934 - 1.25957727
Average (Standard dev.)0.00141309 (±0.21407938)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-20-20-75
Dimensions4040150
Spacing4040150
CellA: 176.48001 Å / B: 176.48001 Å / C: 661.80005 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.4124.4124.412
M x/y/z4040150
origin x/y/z0.0000.0000.000
length x/y/z176.480176.480661.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-207-207-206
NX/NY/NZ414414414
MAP C/R/S123
start NC/NR/NS-20-20-75
NC/NR/NS4040150
D min/max/mean-0.3671.2600.001

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Supplemental data

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Sample components

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Entire : Plasmodium falciparum Actin I

EntireName: Plasmodium falciparum Actin I
Components
  • Sample: Plasmodium falciparum Actin I
  • Protein or peptide: Plasmodium actin I

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Supramolecule #1000: Plasmodium falciparum Actin I

SupramoleculeName: Plasmodium falciparum Actin I / type: sample / ID: 1000 / Number unique components: 1

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Macromolecule #1: Plasmodium actin I

MacromoleculeName: Plasmodium actin I / type: protein_or_peptide / ID: 1 / Recombinant expression: Yes
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm) / Recombinant strain: Sf21
SequenceUniProtKB: Actin I

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statehelical array

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Sample preparation

Concentration0.3 mg/mL
BufferDetails: 50 mM (pH 8.0) Tris-HCl, 500 mM KCl, 20 mM MgCl2, 50 mM DTT, and 10 mM ATP, JAS 5 uM
GridDetails: glow-discharged holey carbon grids (Quantifoil R 2/2)
VitrificationCryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 120 K / Instrument: LEICA EM GP
Method: Polymerized samples were applied in 3-uL aliquots onto freshly glow-discharged holey carbon grids (Quantifoil R 2/2) at 295 K and 70% humidity and vitrified in liquid ethane using a Leica EM ...Method: Polymerized samples were applied in 3-uL aliquots onto freshly glow-discharged holey carbon grids (Quantifoil R 2/2) at 295 K and 70% humidity and vitrified in liquid ethane using a Leica EM GP vitrification robot.

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 69000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 7.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 69000
Sample stageSpecimen holder: 93 K / Specimen holder model: GATAN LIQUID NITROGEN
DateFeb 6, 2013
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 75
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each particle (convolved)
Final reconstructionApplied symmetry - Helical parameters - Δz: 27.69 Å
Applied symmetry - Helical parameters - Δ&Phi: 167.52 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: OTHER / Software - Name: SPRING / Number images used: 3513
DetailsFor 3D structure determination, segments were excised using a regular step size of 70 Angstrom, convolved by their respective CTF and further reconstructed as described (Sachse et al. 2007) using the software SPRING (Desfosses et al. 2014)

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