[English] 日本語
Yorodumi- PDB-5hvk: Crystal structure of LIMK1 mutant D460N in complex with full-leng... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hvk | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of LIMK1 mutant D460N in complex with full-length cofilin-1 | |||||||||
Components |
| |||||||||
Keywords | TRANSFERASE / kinase substrate actin-remodeling | |||||||||
Function / homology | Function and homology information actin filament fragmentation / positive regulation of embryonic development / establishment of spindle localization / positive regulation by host of viral process / positive regulation of actin filament bundle assembly / actin filament severing / regulation of dendritic spine morphogenesis / negative regulation of ubiquitin-protein transferase activity / actin filament depolymerization / RHO GTPases Activate ROCKs ...actin filament fragmentation / positive regulation of embryonic development / establishment of spindle localization / positive regulation by host of viral process / positive regulation of actin filament bundle assembly / actin filament severing / regulation of dendritic spine morphogenesis / negative regulation of ubiquitin-protein transferase activity / actin filament depolymerization / RHO GTPases Activate ROCKs / axon extension / Sema4D induced cell migration and growth-cone collapse / regulation of cell morphogenesis / Fc-gamma receptor signaling pathway involved in phagocytosis / stress fiber assembly / RHO GTPases activate PAKs / lamellipodium membrane / mitotic cytokinesis / Rho protein signal transduction / Sema3A PAK dependent Axon repulsion / positive regulation of axon extension / cytoskeleton organization / positive regulation of stress fiber assembly / EPHB-mediated forward signaling / heat shock protein binding / 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 / ruffle membrane / nuclear matrix / actin filament binding / actin cytoskeleton / Platelet degranulation / lamellipodium / nervous system development / growth cone / actin cytoskeleton organization / vesicle / cytoskeleton / non-specific serine/threonine protein kinase / neuron projection / protein kinase activity / nuclear speck / protein phosphorylation / focal adhesion / protein serine kinase activity / protein serine/threonine kinase activity / negative regulation of apoptotic process / signal transduction / extracellular space / extracellular exosome / ATP binding / membrane / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | |||||||||
Authors | Hamill, S. / Boggon, T.J. | |||||||||
Funding support | United States, 2items
| |||||||||
Citation | Journal: Mol.Cell / Year: 2016 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. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5hvk.cif.gz | 199.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5hvk.ent.gz | 155.2 KB | Display | PDB format |
PDBx/mmJSON format | 5hvk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hv/5hvk ftp://data.pdbj.org/pub/pdb/validation_reports/hv/5hvk | HTTPS FTP |
---|
-Related structure data
Related structure data | 5hvjC 4bexS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-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.) Homo sapiens (human) / Gene: LIMK1, LIMK / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 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.) Homo sapiens (human) / Gene: CFL1, CFL / Plasmid: pET-28a / Details (production host): N-terminal His6-SUMO tag / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P23528 #3: Protein | | Mass: 18431.363 Da / Num. of mol.: 1 / Mutation: A69T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CFL1, CFL / Plasmid: pET-28a / Details (production host): N-terminal His6-SUMO tag / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P23528 #4: Chemical | #5: Chemical | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.08 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å |
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 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| |||||||||||||||||||||||||||||||||||||||||||||||||
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
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|