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- PDB-6i4h: Crystal Structure of Plasmodium falciparum actin I (F54Y mutant) ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6i4h | ||||||||||||
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Title | Crystal Structure of Plasmodium falciparum actin I (F54Y mutant) in the Ca-ATP state | ||||||||||||
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![]() | CONTRACTILE PROTEIN / hydrolase / filamentous / glideosome / cytoskeleton | ||||||||||||
Function / homology | ![]() glial filament / plastid inheritance / schizogony / apical ectoplasmic specialization / basal ectoplasmic specialization / Caspase-mediated cleavage of cytoskeletal proteins / symbiont-mediated actin polymerization-dependent cell-to-cell migration in host / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / striated muscle atrophy / regulation of establishment of T cell polarity ...glial filament / plastid inheritance / schizogony / apical ectoplasmic specialization / basal ectoplasmic specialization / Caspase-mediated cleavage of cytoskeletal proteins / symbiont-mediated actin polymerization-dependent cell-to-cell migration in host / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / 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 / Neutrophil degranulation / regulation of podosome assembly / sequestering of actin monomers / myosin II binding / negative regulation of viral entry into host cell / entry into host cell by a symbiont-containing vacuole / actin filament severing / actin filament capping / actin filament depolymerization / actin polymerization or depolymerization / barbed-end actin filament capping / cell projection assembly / cardiac muscle cell contraction / 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 / phagocytic vesicle / cytoskeleton organization / ruffle / phosphatidylinositol-4,5-bisphosphate binding / response to muscle stretch / cellular response to cadmium ion / actin filament polymerization / Neutrophil degranulation / central nervous system development / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / protein destabilization / structural constituent of cytoskeleton / cellular response to type II interferon / actin filament binding / actin cytoskeleton / lamellipodium / myelin sheath / actin binding / actin cytoskeleton organization / amyloid fibril formation / calcium ion binding / perinuclear region of cytoplasm / ATP hydrolysis activity / protein-containing complex / extracellular space / extracellular region / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Kumpula, E.-P. / Lopez, A.J. / Tajedin, L. / Han, H. / Kursula, I. | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Atomic view into Plasmodium actin polymerization, ATP hydrolysis, and fragmentation. Authors: Kumpula, E.P. / Lopez, A.J. / Tajedin, L. / Han, H. / Kursula, I. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 397 KB | Display | ![]() |
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PDB format | ![]() | 271 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6i4dC ![]() 6i4eC ![]() 6i4fC ![]() 6i4gC ![]() 6i4iC ![]() 6i4jC ![]() 6i4kC ![]() 6i4lC ![]() 6i4mC ![]() 4cbuS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 2 types, 2 molecules AG
#1: Protein | Mass: 42063.676 Da / Num. of mol.: 1 / Mutation: F54Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: PFL2215w / Production host: ![]() ![]() |
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#2: Protein | Mass: 14211.929 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Non-polymers , 5 types, 686 molecules ![](data/chem/img/ATP.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-ATP / | ||||||
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#4: Chemical | #5: Chemical | ChemComp-CL / | #6: Chemical | ChemComp-PEG / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 49.06 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.9 Details: 23% PEG3350, 0.1M BIS-TRIS pH 5.9, 0.2M K-SCN; 20% PEG400 used for cryoprotection |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 9, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→43.75 Å / Num. obs: 206841 / % possible obs: 99.45 % / Redundancy: 3.3 % / Biso Wilson estimate: 18.55 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.05007 / Rpim(I) all: 0.03227 / Rrim(I) all: 0.05975 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.98 / Num. unique obs: 20505 / CC1/2: 0.398 / Rpim(I) all: 0.633 / Rrim(I) all: 1.171 / % possible all: 99.03 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4CBU Resolution: 1.4→43.75 Å / SU ML: 0.1491 / Cross valid method: FREE R-VALUE / σ(F): 0.89 / Phase error: 16.7453
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.61 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→43.75 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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