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Yorodumi- PDB-5ogw: Cryo-EM structure of jasplakinolide-stabilized malaria parasite F... -
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-Basic information
Entry | Database: PDB / ID: 5ogw | |||||||||||||||
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Title | Cryo-EM structure of jasplakinolide-stabilized malaria parasite F-actin at near-atomic resolution | |||||||||||||||
Components | Actin-1 | |||||||||||||||
Keywords | STRUCTURAL PROTEIN / F-actin / Plasmodium / malaria parasite / cytoskeleton / cryo-EM / JAS / Jasplakinolide / filament / glideosome / gliding motility / thin filament | |||||||||||||||
Function / homology | Function and homology information symbiont-mediated actin polymerization-dependent cell-to-cell migration in host / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / hydrolase activity / ATP binding / nucleus / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||||||||
Authors | Pospich, S. / Kumpula, E.-P. / von der Ecken, J. / Vahokoski, J. / Kursula, I. / Raunser, S. | |||||||||||||||
Funding support | Germany, Finland, 4items
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Citation | Journal: 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 / Abstract: During their life cycle, apicomplexan parasites, such as the malaria parasite , use actomyosin-driven gliding motility to move and invade host cells. For this process, actin filament length and ...During their life cycle, apicomplexan parasites, such as the malaria parasite , use actomyosin-driven gliding motility to move and invade host cells. For this process, actin filament length and stability are temporally and spatially controlled. In contrast to canonical actin, actin 1 (Act1) does not readily polymerize into long, stable filaments. The structural basis of filament instability, which plays a pivotal role in host cell invasion, and thus infectivity, is poorly understood, largely because high-resolution structures of Act1 filaments were missing. Here, we report the near-atomic structure of jasplakinolide (JAS)-stabilized Act1 filaments determined by electron cryomicroscopy. The general filament architecture is similar to that of mammalian F-actin. The high resolution of the structure allowed us to identify small but important differences at inter- and intrastrand contact sites, explaining the inherent instability of apicomplexan actin filaments. JAS binds at regular intervals inside the filament to three adjacent actin subunits, reinforcing filament stability by hydrophobic interactions. Our study reveals the high-resolution structure of a small molecule bound to F-actin, highlighting the potential of electron cryomicroscopy for structure-based drug design. Furthermore, our work serves as a strong foundation for understanding the structural design and evolution of actin filaments and their function in motility and host cell invasion of apicomplexan parasites. | |||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5ogw.cif.gz | 372 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ogw.ent.gz | 302.2 KB | Display | PDB format |
PDBx/mmJSON format | 5ogw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ogw_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 5ogw_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 5ogw_validation.xml.gz | 73.1 KB | Display | |
Data in CIF | 5ogw_validation.cif.gz | 101.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/og/5ogw ftp://data.pdbj.org/pub/pdb/validation_reports/og/5ogw | HTTPS FTP |
-Related structure data
Related structure data | 3805MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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-Components
#1: Protein | Mass: 42047.676 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (isolate HB3) (eukaryote) Strain: isolate HB3 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P86287 #2: Chemical | ChemComp-ADP / #3: Chemical | ChemComp-MG / #4: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Plasmodium falciparum actin 1 filament stabilized by jasplakinolide Type: COMPLEX / Details: Filament / Entity ID: #1 / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Plasmodium falciparum HB3 (eukaryote) | ||||||||||||||||||||
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) | ||||||||||||||||||||
Buffer solution | pH: 7.5 Details: 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. | ||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Twist (degree) 167.5 Rise (A) 27.4 | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-2/1 | ||||||||||||||||||||
Vitrification | Instrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 97 % / Chamber temperature: 298 K 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. |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Details: Cs corrected microscope |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2700 nm / Nominal defocus min: 800 nm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 1.5 sec. / Electron dose: 110 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of real images: 1634 |
Image scans | Movie frames/image: 24 / Used frames/image: 1-4 |
-Processing
Software | Name: REFMAC / Version: 5.8.0155 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 144058 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 140716 / Actual pixel size: 1.14 Å / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 3.8→191.52 Å / Cor.coef. Fo:Fc: 0.843 / SU B: 37.916 / SU ML: 0.487 / ESU R: 2.247 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS RIGID BODY FITTED INTO THE ADJACENT DESNITIES CORRESPONDING TO JAS (CHAIN F, H).
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 109.718 Å2
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Refinement step | Cycle: 1 / Total: 14830 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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