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- PDB-5hvk: Crystal structure of LIMK1 mutant D460N in complex with full-leng... -
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Basic information
Entry | Database: PDB / ID: 5hvk | |||||||||
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Title | Crystal structure of LIMK1 mutant D460N in complex with full-length cofilin-1 | |||||||||
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![]() | TRANSFERASE / kinase substrate actin-remodeling | |||||||||
Function / homology | ![]() actin filament fragmentation / positive regulation of embryonic development / establishment of spindle localization / positive regulation of actin filament bundle assembly / negative regulation of ubiquitin-protein transferase activity / actin filament severing / regulation of dendritic spine morphogenesis / positive regulation by host of viral process / actin filament depolymerization / RHO GTPases Activate ROCKs ...actin filament fragmentation / positive regulation of embryonic development / establishment of spindle localization / positive regulation of actin filament bundle assembly / negative regulation of ubiquitin-protein transferase activity / actin filament severing / regulation of dendritic spine morphogenesis / positive regulation by host of viral process / actin filament depolymerization / RHO GTPases Activate ROCKs / regulation of cell morphogenesis / axon extension / Sema4D induced cell migration and growth-cone collapse / Fc-gamma receptor signaling pathway involved in phagocytosis / stress fiber assembly / RHO GTPases activate PAKs / lamellipodium membrane / Rho protein signal transduction / Sema3A PAK dependent Axon repulsion / mitotic cytokinesis / positive regulation of axon extension / positive regulation of stress fiber assembly / cytoskeleton organization / heat shock protein binding / EPHB-mediated forward signaling / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / male germ cell nucleus / response to virus / Regulation of actin dynamics for phagocytic cup formation / nuclear matrix / ruffle membrane / actin filament binding / actin cytoskeleton / Platelet degranulation / lamellipodium / nervous system development / growth cone / actin cytoskeleton organization / vesicle / cytoskeleton / non-specific serine/threonine protein kinase / protein kinase activity / nuclear speck / neuron projection / protein phosphorylation / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / negative regulation of apoptotic process / signal transduction / extracellular space / extracellular exosome / ATP binding / membrane / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Hamill, S. / Boggon, T.J. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Basis for Noncanonical Substrate Recognition of Cofilin/ADF Proteins by LIM Kinases. Authors: Hamill, S. / Lou, H.J. / Turk, B.E. / Boggon, T.J. | |||||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 199.5 KB | Display | ![]() |
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PDB format | ![]() | 155.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1014.7 KB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 34.7 KB | Display | |
Data in CIF | ![]() | 45.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5hvjC ![]() 4bexS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 36473.191 Da / Num. of mol.: 2 / Fragment: UNP residues 329-638 / Mutation: D460N Source method: isolated from a genetically manipulated source Details: Optimized cDNA / Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P53667, non-specific serine/threonine protein kinase #2: Protein | | Mass: 18511.342 Da / Num. of mol.: 1 / Mutation: A69T Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | | Mass: 18431.363 Da / Num. of mol.: 1 / Mutation: A69T Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Chemical | #5: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.08 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 1.2-1.4 M tri-Sodium citrate, 0.1 M sodium acetate, pH 5.5. 4 crystals used. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 28, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→50 Å / Num. obs: 15631 / % possible obs: 100 % / Redundancy: 10.1 % / Biso Wilson estimate: 33.7 Å2 / CC1/2: 0.531 / Rmerge(I) obs: 0.54 / Net I/σ(I): 2.5 |
Reflection shell | Resolution: 3.5→3.63 Å / Redundancy: 8.5 % / Mean I/σ(I) obs: 1.3 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4BEX Resolution: 3.5→48.112 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.13 / 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: 3.5→48.112 Å
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Refine LS restraints |
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LS refinement shell |
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