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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
ComponentsActin-1
KeywordsSTRUCTURAL PROTEIN / F-actin / Plasmodium / malaria parasite / cytoskeleton / cryo-EM / JAS / Jasplakinolide / filament / glideosome / gliding motility / thin filament / structural protein
Function / homologyActin, conserved site / Actin family / Actin/actin-like conserved site / Actin / Actins signature 1. / Actins signature 2. / Actins and actin-related proteins signature. / actin polymerization-dependent cell motility involved in migration of symbiont in host / actin filament / structural constituent of cytoskeleton ...Actin, conserved site / Actin family / Actin/actin-like conserved site / Actin / Actins signature 1. / Actins signature 2. / Actins and actin-related proteins signature. / actin polymerization-dependent cell motility involved in migration of symbiont in host / actin filament / structural constituent of cytoskeleton / ATP binding / cytoplasm / Actin-1
Function and homology information
Specimen sourcePlasmodium falciparum (malaria parasite P. falciparum)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.8 Å resolution
AuthorsPospich, S. / Kumpula, E.-P. / von der Ecken, J. / Vahokoski, J. / Kursula, I. / Raunser, S.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Near-atomic structure of jasplakinolide-stabilized malaria parasite F-actin reveals the structural basis of filament instability.
Authors: 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
RevisionDateData content typeGroupCategoryItemProviderType
1.0Sep 27, 2017Structure modelrepositoryInitial release
1.1Nov 8, 2017Structure modelData processing / Database referencescitation / em_software_citation.journal_volume / _citation.page_first / _citation.page_last / _em_software.name

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Structure visualization

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Structure viewerMolecule:
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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: Protein/peptide
Actin-1 / / Actin I / PfACT1


Mass: 42047.676 Da / Num. of mol.: 5
Source: (gene. exp.) Plasmodium falciparum (isolate HB3) (eukaryote)
Strain: isolate HB3 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P86287
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 5 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Formula: Mg / Magnesium
#4: Chemical ChemComp-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 reconstruction

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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 (eukaryote)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
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.FormulaBuffer ID
110 mMHEPES1
20.2 mMCaCl21
350 mMKCl1
45 mMDTT1
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 FIELDBright-field microscopy / 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
IDNameVersionCategoryDetails
2SPARXv3.0particle selectionsxhelixboxer.py
1EPUimage acquisition
4CTFFIND4.0.7CTF correction
5RELION1.4CTF correction
8MODELLERmodel fittinghomology modelling
9UCSF Chimeramodel fittingrigid body fitting
10iMODFITmodel fittingflexible fitting
12Cootmodel refinementmanual building
13PHENIXmodel refinementinital refinement
14REFMACmodel refinementfinal refinement
15RELION1.4initial Euler assignment
16RELION1.4final Euler assignment
18RELION1.43D reconstruction
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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