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- EMDB-3805: Cryo-EM structure of jasplakinolide-stabilized malaria parasite F... -

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Basic information

Entry
Database: EMDB / ID: 3805
TitleCryo-EM structure of jasplakinolide-stabilized malaria parasite F-actin at near-atomic resolution
SamplePlasmodium falciparum actin 1 filament stabilized by jasplakinolide
SourcePlasmodium falciparum hb3 / eukaryote / image: Plasmodium falciparum
Map data
Methodsingle particle reconstruction, at 3.8 Å resolution
AuthorsPospich S / Kumpula E-P
CitationProc. Natl. Acad. Sci. U.S.A., 2017, 114, 10636-10641

Proc. Natl. Acad. Sci. U.S.A., 2017, 114, 10636-10641 Yorodumi Papers
Near-atomic structure of jasplakinolide-stabilized malaria parasite F-actin reveals the structural basis of filament instability.
Sabrina Pospich / Esa-Pekka Kumpula / Julian von der Ecken / Juha Vahokoski / Inari Kursula / Stefan Raunser

Validation ReportPDB-ID: 5ogw

SummaryFull reportAbout validation report
DateDeposition: Jul 13, 2017 / Header (metadata) release: Jul 26, 2017 / Map release: Sep 27, 2017 / Last update: Nov 8, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.09
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.09
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5ogw
  • Surface level: 0.09
  • Imaged by UCSF CHIMERA
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5ogw
  • Imaged by Jmol
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Supplemental images

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Map

Fileemd_3805.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.14 Å/pix.
= 291.84 Å
256 pix
1.14 Å/pix.
= 291.84 Å
256 pix
1.14 Å/pix.
= 291.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.14 Å
Density
Contour Level:0.09 (by author), 0.09 (movie #1):
Minimum - Maximum-0.15085225 - 0.3457834
Average (Standard dev.)0.0014830945 (0.013865351)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin000
Limit255255255
Spacing256256256
CellA=B=C: 291.84 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.141.141.14
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z291.840291.840291.840
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.1510.3460.001

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Supplemental data

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Mask #1

Fileemd_3805_msk_1.map ( map file in CCP4 format, 67109 KB )
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms
Data typeImage stored as Reals
Space group number1

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Mask #1~

Fileemd_3805_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Sample components

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Entire Plasmodium falciparum actin 1 filament stabilized by jasplakinolide

EntireName: Plasmodium falciparum actin 1 filament stabilized by jasplakinolide
Details: Filament / Number of components: 5

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Component #1: protein, Plasmodium falciparum actin 1 filament stabilized by jas...

ProteinName: Plasmodium falciparum actin 1 filament stabilized by jasplakinolide
Details: Filament / Recombinant expression: No
SourceSpecies: Plasmodium falciparum hb3 / eukaryote / image: Plasmodium falciparum
Source (engineered)Expression System: Spodoptera frugiperda / arthropod

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Component #2: protein, Actin-1

ProteinName: Actin-1 / Recombinant expression: No
MassTheoretical: 42.047676 kDa
Source (engineered)Expression System: Plasmodium falciparum (isolate hb3) / eukaryote /
Strain: isolate HB3

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

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

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Component #4: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #5: ligand, Jasplakinolide

LigandName: Jasplakinolide / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 0.70967 kDa

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Experimental details

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Sample preparation

Specimen statefilament
Sample solutionBuffer solution: 10 mM HEPES pH 7.5, 0.2 mM CaCl2, 50 mM KCl, 4 mM MgCl2, 5 mM DTT and 0.5 mM ATP. JAS was added at a 1:1 molar ratio during polyermization.
pH: 7.5
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Temperature: 298 K / Humidity: 97 %
Details: Sample (2 uL of JAS-stabilized F-actin solution) was applied to a glow-discharged holey carbon grid, incubated for 30 s and manually blotted for 4 s from the backside with filter paper.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS / Details: Cs corrected microscope
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 110 e/Å2 / Illumination mode: SPOT SCAN
LensImaging mode: BRIGHT FIELD / Defocus: 800 - 2700 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 1634

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 140716
3D reconstructionSoftware: RELION / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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