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- PDB-5ogw: Cryo-EM structure of jasplakinolide-stabilized malaria parasite F... -

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Basic information

Entry
Database: PDB / ID: 5ogw
TitleCryo-EM structure of jasplakinolide-stabilized malaria parasite F-actin at near-atomic resolution
DescriptorActin-1
KeywordsSTRUCTURAL PROTEIN / F-actin / Plasmodium / malaria parasite / cytoskeleton / cryo-EM / JAS / Jasplakinolide / filament / glideosome / gliding motility / thin filament / structural protein
Specimen sourcePlasmodium falciparum (isolate hb3) / eukaryote /
MethodElectron microscopy (3.8 Å resolution / Filament / Single particle)
AuthorsPospich, S. / Kumpula, E.-P. / von der Ecken, J. / Vahokoski, J. / Kursula, I. / Raunser, S.
CitationProc. Natl. Acad. Sci. U.S.A., 2017

Proc. Natl. Acad. Sci. U.S.A., 2017 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 Report
SummaryFull reportAbout validation report
DateDeposition: Jul 13, 2017 / Release: Sep 27, 2017

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Assembly

Deposited unit
A: Actin-1
B: Actin-1
C: Actin-1
D: Actin-1
E: Actin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,62518
Polyers210,2385
Non-polymers4,38713
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

#1: Polypeptide(L)
Actin-1 / Actin I / PfACT1


Mass: 42047.676 Da / Num. of mol.: 5
Source: (gene. exp.) Plasmodium falciparum (isolate hb3) / eukaryote /
References: UniProt: P86287
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / ADP *YM


Mass: 427.201 Da / Num. of mol.: 5 / Formula: C10H15N5O10P2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Formula: Mg
#4: ChemicalChemComp-9UE / Jasplakinolide


Mass: 709.670 Da / Num. of mol.: 3 / Formula: C36H45BrN4O6

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: Plasmodium falciparum actin 1 filament stabilized by jasplakinolide
Type: COMPLEX / Details: Filament / Entity ID: 1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Plasmodium falciparum HB3
Source (recombinant)Organism: Spodoptera frugiperda
Buffer solutionDetails: 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
Buffer component
IDConc.UnitsFormulaBuffer ID
110mMHEPES1
20.2mMCaCl21
350mMKCl1
45mMDTT1
SpecimenDetails: Twist (degree) 167.5 Rise (A) 27.4 / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 / Grid type: C-flat-2/1
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 97 % / Chamber temperature: 298 kelvins
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
MicroscopyMicroscope model: FEI TITAN KRIOS / Details: Cs corrected microscope
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2700 nm / Nominal defocus min: 800 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.5 sec. / Electron dose: 110 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Number of real images: 1634
Image scansMovie frames/image: 24 / Used frames/image: 1-4

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Processing

SoftwareName: REFMAC / Version: 5.8.0155 / Classification: refinement
EM software
IDNameVersionCategoryDetailsImage processing IDImaging IDFitting ID
2SPARXv3.0PARTICLE SELECTIONsxhelixboxer.py1
1EPUIMAGE ACQUISITION1
4CTFFIND4.0.7CTF CORRECTION1
5RELION1.4CTF CORRECTION1
8MODELLERMODEL FITTINGhomology modelling1
9UCSF ChimeraMODEL FITTINGrigid body fitting1
10iModFitMODEL FITTINGflexible fitting1
12CootMODEL REFINEMENTmanual building1
13PHENIXMODEL REFINEMENTinital refinement1
14REFMACMODEL REFINEMENTfinal refinement1
15RELION1.4INITIAL EULER ASSIGNMENT1
16RELION1.4FINAL EULER ASSIGNMENT1
18RELION1.4RECONSTRUCTION1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 144058
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 140716 / Actual pixel size: 1.14 / Symmetry type: POINT
Refine
Refine IDB iso meanAniso B11Aniso B12Aniso B13Aniso B22Aniso B23Aniso B33Correlation coeff Fo to FcDetailsR factor R workR factor obsHighest resolutionLowest resolutionNumber reflection obsPercent reflection obsOverall SU BOverall SU MLOverall ESU RSolvent ion probe radiiSolvent shrinkage radiiSolvent vdw probe radiiStereochemistry target valuesSolvent model details
1109.7180.760.170.221.38-0.39-2.140.843HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS RIGID BODY FITTED INTO THE ADJACENT DESNITIES CORRESPONDING TO JAS (CHAIN F, H).0.326800.326803.80191.5263851100.0037.9160.4872.2470.800.801.20MAXIMUM LIKELIHOOD WITH PHASESMASK
ELECTRON MICROSCOPY
Number of atoms included #1Total: 14830
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0100.01915155
ELECTRON MICROSCOPYr_bond_other_d0.0040.02014325
ELECTRON MICROSCOPYr_angle_refined_deg1.3741.97420560
ELECTRON MICROSCOPYr_angle_other_deg1.1293.00033105
ELECTRON MICROSCOPYr_dihedral_angle_1_deg6.6485.0001845
ELECTRON MICROSCOPYr_dihedral_angle_2_deg23.84224.186645
ELECTRON MICROSCOPYr_dihedral_angle_3_deg8.41615.0002595
ELECTRON MICROSCOPYr_dihedral_angle_4_deg9.30215.00090
ELECTRON MICROSCOPYr_chiral_restr0.0750.2002270
ELECTRON MICROSCOPYr_gen_planes_refined0.0060.02117425
ELECTRON MICROSCOPYr_gen_planes_other0.0030.0203290
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it6.52310.4617395
ELECTRON MICROSCOPYr_mcbond_other6.52310.4617394
ELECTRON MICROSCOPYr_mcangle_it10.79215.7019235
ELECTRON MICROSCOPYr_mcangle_other10.79115.7029236
ELECTRON MICROSCOPYr_scbond_it7.93211.5807760
ELECTRON MICROSCOPYr_scbond_other7.93211.5807761
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other13.40016.97511326
ELECTRON MICROSCOPYr_long_range_B_refined20.05345725
ELECTRON MICROSCOPYr_long_range_B_other20.05345726
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS restraints ncs

Refine ID: ELECTRON MICROSCOPY / Type: tight thermal / Weight position: 0.5

Dom IDAuth asym IDEns IDNumberRms dev position
1A157408.72
1B157408.70
1C1574012.37
1D157408.21
1E157407.26
2A29112.94
2B29110.94
2C29112.68
2D29132.37
2E2917.79
Refine LS shellHighest resolution: 3.8 Å / R factor R work: 0.564 / Lowest resolution: 3.899 Å / Number reflection R free: 0 / Number reflection R work: 4675 / Total number of bins used: 20 / Percent reflection obs: 1

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