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Yorodumi- PDB-4cbw: Crystal structure of Plasmodium berghei actin I with D-loop from ... -
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-Basic information
Entry | Database: PDB / ID: 4cbw | |||||||||
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Title | Crystal structure of Plasmodium berghei actin I with D-loop from muscle actin | |||||||||
Components |
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Keywords | MOTOR PROTEIN / MALARIA / MOTILITY / PARASITE | |||||||||
Function / homology | Function and homology information glial filament / apical ectoplasmic specialization / basal ectoplasmic specialization / 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 ...glial filament / apical ectoplasmic specialization / basal ectoplasmic specialization / 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 / 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 / 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 / protein-containing complex / extracellular space / extracellular region / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | PLASMODIUM BERGHEI (eukaryote) SYNTHETIC CONSTRUCT (others) MUS MUSCULUS (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.501 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 | 4cbw.cif.gz | 298.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cbw.ent.gz | 244.8 KB | Display | PDB format |
PDBx/mmJSON format | 4cbw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cbw_validation.pdf.gz | 743 KB | Display | wwPDB validaton report |
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Full document | 4cbw_full_validation.pdf.gz | 747.3 KB | Display | |
Data in XML | 4cbw_validation.xml.gz | 19.2 KB | Display | |
Data in CIF | 4cbw_validation.cif.gz | 25.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cb/4cbw ftp://data.pdbj.org/pub/pdb/validation_reports/cb/4cbw | HTTPS FTP |
-Related structure data
Related structure data | 2572C 4cbuSC 4cbxC S: Starting model for refinement C: citing same article (ref.) |
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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: 41944.480 Da / Num. of mol.: 1 Fragment: ACTIN RESIDUES 2-39, ALPHA SKELETAL MUSCLE RESIDUES 40-61, Source method: isolated from a genetically manipulated source Details: RESIDUES 40-61 REPLACED BY THOSE OF SKELETAL MUSCLE ACTIN Source: (gene. exp.) PLASMODIUM BERGHEI (eukaryote), (gene. exp.) SYNTHETIC CONSTRUCT (others) Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Strain (production host): SF21 / References: UniProt: Q4Z1L3 |
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#2: Protein | Mass: 14211.929 Da / Num. of mol.: 1 / Fragment: G1 DOMAIN, RESIDUES 25-149 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: P13020 |
-Non-polymers , 4 types, 61 molecules
#3: Chemical | #4: Chemical | ChemComp-DIO / | #5: Chemical | ChemComp-ATP / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 58 % / Description: NONE |
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Crystal grow | pH: 8 Details: 100 MM TRIS-HCL (PH 8.0), 8% (W/V), PEG 20000, 2% (V/V) DIOXANE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.92 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 1, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→38.5 Å / Num. obs: 24163 / % possible obs: 99.6 % / Observed criterion σ(I): -1 / Redundancy: 6.7 % / Biso Wilson estimate: 55.19 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 4.1 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 0.9 / % possible all: 96.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4CBU Resolution: 2.501→38.581 Å / SU ML: 0.36 / σ(F): 1.37 / Phase error: 32.92 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 75 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.501→38.581 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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