+Open data
-Basic information
Entry | Database: PDB / ID: 4cbx | ||||||
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Title | Crystal structure of Plasmodium berghei actin II | ||||||
Components |
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Keywords | MOTOR PROTEIN / MALARIA / MOTILITY / PARASITE | ||||||
Function / homology | Function and homology information positive regulation of development of symbiont in host / exit from host cell / glial filament / apical ectoplasmic specialization / basal ectoplasmic specialization / male gamete generation / Caspase-mediated cleavage of cytoskeletal proteins / striated muscle atrophy / regulation of establishment of T cell polarity / regulation of plasma membrane raft polarization ...positive regulation of development of symbiont in host / exit from host cell / glial filament / apical ectoplasmic specialization / basal ectoplasmic specialization / male gamete generation / Caspase-mediated cleavage of cytoskeletal proteins / striated muscle atrophy / regulation of establishment of T cell polarity / regulation of plasma membrane raft polarization / regulation of receptor clustering / renal protein absorption / positive regulation of keratinocyte apoptotic process / positive regulation of protein processing in phagocytic vesicle / positive regulation of actin nucleation / phosphatidylinositol 3-kinase catalytic subunit binding / actin cap / cilium organization / regulation of podosome assembly / sequestering of actin monomers / myosin II binding / negative regulation of viral entry into host cell / actin filament severing / actin filament capping / actin filament depolymerization / barbed-end actin filament capping / actin polymerization or depolymerization / cardiac muscle cell contraction / cell projection assembly / podosome / relaxation of cardiac muscle / positive regulation of p38MAPK cascade / phagocytosis, engulfment / positive regulation of cardiac muscle hypertrophy / hepatocyte apoptotic process / sarcoplasm / cilium assembly / vesicle-mediated transport / ruffle / cellular response to cadmium ion / response to muscle stretch / phosphatidylinositol-4,5-bisphosphate binding / phagocytic vesicle / actin filament polymerization / Neutrophil degranulation / central nervous system development / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / protein destabilization / cellular response to type II interferon / actin filament binding / actin cytoskeleton / lamellipodium / myelin sheath / actin binding / actin cytoskeleton organization / amyloid fibril formation / cytoskeleton / calcium ion binding / perinuclear region of cytoplasm / ATP hydrolysis activity / protein-containing complex / extracellular space / extracellular region / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | PLASMODIUM BERGHEI (eukaryote) MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Vahokoski, J. / Bhargav, S.P. / Desfosses, A. / Andreadaki, M. / Kumpula, E.P. / Ignatev, A. / Munico Martinez, S. / Lepper, S. / Frischknecht, F. / Siden-Kiamos, I. ...Vahokoski, J. / Bhargav, S.P. / Desfosses, A. / Andreadaki, M. / Kumpula, E.P. / Ignatev, A. / Munico Martinez, S. / Lepper, S. / Frischknecht, F. / Siden-Kiamos, I. / Sachse, C. / Kursula, I. | ||||||
Citation | Journal: PLoS Pathog / Year: 2014 Title: Structural differences explain diverse functions of Plasmodium actins. Authors: Juha Vahokoski / Saligram Prabhakar Bhargav / Ambroise Desfosses / Maria Andreadaki / Esa-Pekka Kumpula / Silvia Muñico Martinez / Alexander Ignatev / Simone Lepper / Friedrich Frischknecht ...Authors: Juha Vahokoski / Saligram Prabhakar Bhargav / Ambroise Desfosses / Maria Andreadaki / Esa-Pekka Kumpula / Silvia Muñico Martinez / Alexander Ignatev / Simone Lepper / Friedrich Frischknecht / Inga Sidén-Kiamos / Carsten Sachse / Inari Kursula / Abstract: Actins are highly conserved proteins and key players in central processes in all eukaryotic cells. The two actins of the malaria parasite are among the most divergent eukaryotic actins and also ...Actins are highly conserved proteins and key players in central processes in all eukaryotic cells. The two actins of the malaria parasite are among the most divergent eukaryotic actins and also differ from each other more than isoforms in any other species. Microfilaments have not been directly observed in Plasmodium and are presumed to be short and highly dynamic. We show that actin I cannot complement actin II in male gametogenesis, suggesting critical structural differences. Cryo-EM reveals that Plasmodium actin I has a unique filament structure, whereas actin II filaments resemble canonical F-actin. Both Plasmodium actins hydrolyze ATP more efficiently than α-actin, and unlike any other actin, both parasite actins rapidly form short oligomers induced by ADP. Crystal structures of both isoforms pinpoint several structural changes in the monomers causing the unique polymerization properties. Inserting the canonical D-loop to Plasmodium actin I leads to the formation of long filaments in vitro. In vivo, this chimera restores gametogenesis in parasites lacking actin II, suggesting that stable filaments are required for exflagellation. Together, these data underline the divergence of eukaryotic actins and demonstrate how structural differences in the monomers translate into filaments with different properties, implying that even eukaryotic actins have faced different evolutionary pressures and followed different paths for developing their polymerization properties. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cbx.cif.gz | 220.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cbx.ent.gz | 174 KB | Display | PDB format |
PDBx/mmJSON format | 4cbx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cbx_validation.pdf.gz | 783.6 KB | Display | wwPDB validaton report |
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Full document | 4cbx_full_validation.pdf.gz | 787.9 KB | Display | |
Data in XML | 4cbx_validation.xml.gz | 23.5 KB | Display | |
Data in CIF | 4cbx_validation.cif.gz | 34 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cb/4cbx ftp://data.pdbj.org/pub/pdb/validation_reports/cb/4cbx | HTTPS FTP |
-Related structure data
Related structure data | 2572C 4cbuC 4cbwC 1p8zS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AG
#1: Protein | Mass: 42856.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PLASMODIUM BERGHEI (eukaryote) / Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q4YU79 |
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#2: Protein | Mass: 14211.929 Da / Num. of mol.: 1 / Fragment: G1 DOMAIN, RESIDUES 50-174 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): ROSETTA / References: UniProt: P13020 |
-Non-polymers , 6 types, 356 molecules
#3: Chemical | ChemComp-ATP / | ||||||||
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#4: Chemical | #5: Chemical | ChemComp-NA / | #6: Chemical | #7: Chemical | ChemComp-PO4 / | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 18% (W/V) PEG 8000, 0.2 M AMMONIUM SULFATE, 0.1 M BIS-TRIS PROPANE PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 |
Detector | Type: PLATINUM135 / Detector: CCD / Date: Aug 17, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→32 Å / Num. obs: 29458 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 27.62 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 5.6 |
Reflection shell | Resolution: 2.2→2.25 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 0.9 / % possible all: 95.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1P8Z Resolution: 2.2→31.907 Å / SU ML: 0.25 / σ(F): 1.36 / Phase error: 22.27 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→31.907 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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