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- PDB-3lk2: Crystal structure of CapZ bound to the uncapping motif from CARMIL -
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Open data
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Basic information
Entry | Database: PDB / ID: 3lk2 | ||||||
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Title | Crystal structure of CapZ bound to the uncapping motif from CARMIL | ||||||
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![]() | PROTEIN BINDING / CapZ / CARMIL / actin filaments / uncapping / actin-filament regulators / protein-protein complex / Actin capping / Actin-binding / Cytoskeleton | ||||||
Function / homology | ![]() barbed-end actin filament uncapping / positive regulation of lamellipodium organization / negative regulation of barbed-end actin filament capping / Advanced glycosylation endproduct receptor signaling / RHOD GTPase cycle / RHOF GTPase cycle / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-independent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / macropinosome ...barbed-end actin filament uncapping / positive regulation of lamellipodium organization / negative regulation of barbed-end actin filament capping / Advanced glycosylation endproduct receptor signaling / RHOD GTPase cycle / RHOF GTPase cycle / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-independent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / macropinosome / Factors involved in megakaryocyte development and platelet production / actin filament network formation / WASH complex / : / F-actin capping protein complex / macropinocytosis / urate metabolic process / negative regulation of filopodium assembly / regulation of Arp2/3 complex-mediated actin nucleation / cell junction assembly / ruffle organization / barbed-end actin filament capping / actin polymerization or depolymerization / regulation of cell morphogenesis / regulation of lamellipodium assembly / lamellipodium assembly / cortical cytoskeleton / positive regulation of actin filament polymerization / cell leading edge / filamentous actin / brush border / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of stress fiber assembly / cytoskeleton organization / hippocampal mossy fiber to CA3 synapse / actin filament organization / Schaffer collateral - CA1 synapse / cell morphogenesis / Z disc / actin filament binding / cell migration / lamellipodium / Factors involved in megakaryocyte development and platelet production / actin cytoskeleton organization / postsynaptic density / positive regulation of cell migration / nuclear speck / protein-containing complex binding / extracellular exosome / nucleoplasm / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hernandez-Valladares, M. / Kim, T. / Kannan, B. / Tung, A. / Aguda, A.H. / Larsson, M. / Cooper, J.A. / Robinson, R.C. | ||||||
![]() | ![]() Title: Structural characterization of a capping protein interaction motif defines a family of actin filament regulators. Authors: Hernandez-Valladares, M. / Kim, T. / Kannan, B. / Tung, A. / Aguda, A.H. / Larsson, M. / Cooper, J.A. / Robinson, R.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 127 KB | Display | ![]() |
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PDB format | ![]() | 97.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 447.1 KB | Display | ![]() |
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Full document | ![]() | 455.8 KB | Display | |
Data in XML | ![]() | 24.2 KB | Display | |
Data in CIF | ![]() | 34.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3lk3C ![]() 3lk4C ![]() 1iznS S: Starting model for refinement C: citing same article ( |
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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
#1: Protein | Mass: 33001.789 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 27315.877 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Protein | Mass: 5920.755 Da / Num. of mol.: 1 / Fragment: CPI, capping protein interacting motif / Source method: obtained synthetically Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Homo sapiens (human) References: UniProt: Q5VZK9 |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.35 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 10% w/v PEG 20000, 100mM MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 14, 2008 / Details: phosphor screen, fiber-optic taper and CCD chip |
Radiation | Monochromator: double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. all: 31702 / Num. obs: 31671 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 40.9 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 20.4 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 8.1 / Num. unique all: 1514 / Rsym value: 0.37 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1IZN Resolution: 2.2→19.71 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.912 / SU B: 14.784 / SU ML: 0.17 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.298 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→19.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.256 Å / Total num. of bins used: 20
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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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