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- PDB-3a5n: Crystal Structure of a Dictyostelium P109A Ca2+-Actin in Complex ... -
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Basic information
Entry | Database: PDB / ID: 3a5n | ||||||
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Title | Crystal Structure of a Dictyostelium P109A Ca2+-Actin in Complex with Human Gelsolin Segment 1 | ||||||
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![]() | CONTRACTILE PROTEIN / ACTIN / ADP / HYDROLYSIS / ACTIN CAPPING / ACTIN-BINDING / CYTOSKELETON / ATP-BINDING / NUCLEOTIDE-BINDING / STRUCTURAL PROTEIN | ||||||
Function / homology | ![]() intranuclear rod / phototaxis / leading edge of lamellipodium / macropinocytic cup / phagolysosome / striated muscle atrophy / regulation of establishment of T cell polarity / regulation of plasma membrane raft polarization / regulation of receptor clustering / renal protein absorption ...intranuclear rod / phototaxis / leading edge of lamellipodium / macropinocytic cup / phagolysosome / 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 / cell pole / positive regulation of actin nucleation / phosphatidylinositol 3-kinase catalytic subunit binding / positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / actin cap / regulation of podosome assembly / sequestering of actin monomers / myosin II binding / negative regulation of viral entry into host cell / actin filament severing / plasma membrane repair / actin filament capping / actin filament depolymerization / barbed-end actin filament capping / actin polymerization or depolymerization / early phagosome / cardiac muscle cell contraction / hyperosmotic response / cell projection assembly / podosome / Sensory processing of sound by outer hair cells of the cochlea / relaxation of cardiac muscle / cortical actin cytoskeleton / phagocytosis, engulfment / myosin binding / hepatocyte apoptotic process / cell leading edge / pseudopodium / phagocytic cup / sarcoplasm / mitotic cytokinesis / endocytic vesicle / cilium assembly / Caspase-mediated cleavage of cytoskeletal proteins / phagocytosis / vesicle-mediated transport / response to cAMP / response to muscle stretch / phosphatidylinositol-4,5-bisphosphate binding / phagocytic vesicle / actin filament polymerization / lipid droplet / central nervous system development / actin filament / actin filament organization / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / protein destabilization / cell morphogenesis / structural constituent of cytoskeleton / cellular response to type II interferon / endocytosis / chemotaxis / cell-cell junction / actin filament binding / actin cytoskeleton / lamellipodium / actin binding / cell cortex / secretory granule lumen / ficolin-1-rich granule lumen / amyloid fibril formation / blood microparticle / hydrolase activity / Amyloid fiber formation / focal adhesion / calcium ion binding / Neutrophil degranulation / positive regulation of gene expression / extracellular space / extracellular exosome / extracellular region / ATP binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Murakami, K. / Yasunaga, T. / Noguchi, T.Q. / Uyeda, T.Q. / Wakabayashi, T. | ||||||
![]() | ![]() Title: Structural basis for actin assembly, activation of ATP hydrolysis, and delayed phosphate release. Authors: Kenji Murakami / Takuo Yasunaga / Taro Q P Noguchi / Yuki Gomibuchi / Kien X Ngo / Taro Q P Uyeda / Takeyuki Wakabayashi / ![]() Abstract: Assembled actin filaments support cellular signaling, intracellular trafficking, and cytokinesis. ATP hydrolysis triggered by actin assembly provides the structural cues for filament turnover in vivo. ...Assembled actin filaments support cellular signaling, intracellular trafficking, and cytokinesis. ATP hydrolysis triggered by actin assembly provides the structural cues for filament turnover in vivo. Here, we present the cryo-electron microscopic (cryo-EM) structure of filamentous actin (F-actin) in the presence of phosphate, with the visualization of some α-helical backbones and large side chains. A complete atomic model based on the EM map identified intermolecular interactions mediated by bound magnesium and phosphate ions. Comparison of the F-actin model with G-actin monomer crystal structures reveals a critical role for bending of the conserved proline-rich loop in triggering phosphate release following ATP hydrolysis. Crystal structures of G-actin show that mutations in this loop trap the catalytic site in two intermediate states of the ATPase cycle. The combined structural information allows us to propose a detailed molecular mechanism for the biochemical events, including actin polymerization and ATPase activation, critical for actin filament dynamics. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 122.4 KB | Display | ![]() |
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PDB format | ![]() | 91.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 762.6 KB | Display | ![]() |
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Full document | ![]() | 771.1 KB | Display | |
Data in XML | ![]() | 24.4 KB | Display | |
Data in CIF | ![]() | 35.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1674C ![]() 3a5lC ![]() 3a5mC ![]() 3a5oC ![]() 3g37C ![]() 1c0gS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 14205.001 Da / Num. of mol.: 1 / Fragment: GELSOLIN-LIKE 1, residues 53-176 / Mutation: N35C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Protein | Mass: 41432.203 Da / Num. of mol.: 1 / Mutation: P109A/E208A/R206A/E207A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
#3: Chemical | #4: Chemical | ChemComp-ATP / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 22, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→6 Å / Num. obs: 29796 / Biso Wilson estimate: 34.3 Å2 / Rmerge(I) obs: 0.183 |
Reflection shell | Resolution: 2.35→2.44 Å / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 3.97 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1C0G Resolution: 2.36→6 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.926 / Occupancy max: 1 / Occupancy min: 0 / SU B: 5.878 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.349 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 max: 87.86 Å2 / Biso mean: 26.887 Å2 / Biso min: 6.63 Å2
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Refinement step | Cycle: LAST / Resolution: 2.36→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.36→2.42 Å / Total num. of bins used: 20
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