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- EMDB-10588: Plasmodium falciparum Act2 filament structure -

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Basic information

Entry
Database: EMDB / ID: EMD-10588
TitlePlasmodium falciparum Act2 filament structure
Map data
Sample
  • Complex: PfAct2
Function / homology
Function and homology information


symbiont-mediated actin polymerization-dependent cell-to-cell migration in host / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Neutrophil degranulation / microfilament motor activity / cytoskeleton organization / actin filament / structural constituent of cytoskeleton / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / actin cytoskeleton / hydrolase activity ...symbiont-mediated actin polymerization-dependent cell-to-cell migration in host / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Neutrophil degranulation / microfilament motor activity / cytoskeleton organization / actin filament / structural constituent of cytoskeleton / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / actin cytoskeleton / hydrolase activity / ATP binding / cytoplasm
Similarity search - Function
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 3D7 (eukaryote)
Methodhelical reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsVahokoski J / Calder LJ / Lopez AJ / Rosenthal PB / Kursula I
CitationJournal: To Be Published
Title: The structure and biochemical properties of PfAct2
Authors: Lopez AJ / Vahokoski J / Tajedin L / Calder LJ / Rosenthal PB / Kursula I
History
DepositionJan 3, 2020-
Header (metadata) releaseJan 13, 2021-
Map releaseJan 13, 2021-
UpdateApr 14, 2021-
Current statusApr 14, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10588.png

Downloads & links

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Map

FileDownload / File: emd_10588.map.gz / Format: CCP4 / Size: 134.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 328 pix.
= 357.52 Å		1.09 Å/pix.
x 328 pix.
= 357.52 Å		1.09 Å/pix.
x 328 pix.
= 357.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.10538166 - 0.22179927
Average (Standard dev.)0.00030934456 (±0.0060575893)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions328328328
Spacing328328328
CellA=B=C: 357.52002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z328328328
origin x/y/z0.0000.0000.000
length x/y/z357.520357.520357.520
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS328328328
D min/max/mean-0.1050.2220.000

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Supplemental data

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Mask #1

Fileemd_10588_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: A full-map from Relion autorefine

Fileemd_10588_additional_1.map
AnnotationA full-map from Relion autorefine
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_10588_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_10588_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : PfAct2

EntireName: PfAct2
Components
  • Complex: PfAct2

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Supramolecule #1: PfAct2

SupramoleculeName: PfAct2 / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm) / Recombinant strain: Sf21

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 47.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / 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: 28.3109 Å
Applied symmetry - Helical parameters - Δ&Phi: -166.901 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1beta a7b0bd) / Number images used: 47197
CTF correctionSoftware - Name: CTFFIND (ver. 4.1.10)
Startup modelType of model: NONE / Details: a cylinder
Final angle assignmentType: NOT APPLICABLE

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