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Open data
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Basic information
Entry | Database: PDB / ID: 6lca | ||||||
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Title | Crystal structure of human Dishevelled1 PDZ domain homotrimer | ||||||
![]() | Segment polarity protein dishevelled homolog DVL-1 | ||||||
![]() | SIGNALING PROTEIN / Wnt signaling pathway / Developmental protein / PROTEIN BINDING / Dvl | ||||||
Function / homology | ![]() positive regulation of protein localization to presynapse / Negative regulation of TCF-dependent signaling by DVL-interacting proteins / convergent extension involved in neural plate elongation / skeletal muscle acetylcholine-gated channel clustering / planar cell polarity pathway involved in neural tube closure / cochlea morphogenesis / protein localization to microtubule / non-canonical Wnt signaling pathway / positive regulation of neuron projection arborization / presynapse assembly ...positive regulation of protein localization to presynapse / Negative regulation of TCF-dependent signaling by DVL-interacting proteins / convergent extension involved in neural plate elongation / skeletal muscle acetylcholine-gated channel clustering / planar cell polarity pathway involved in neural tube closure / cochlea morphogenesis / protein localization to microtubule / non-canonical Wnt signaling pathway / positive regulation of neuron projection arborization / presynapse assembly / collateral sprouting / WNT5:FZD7-mediated leishmania damping / neurotransmitter secretion / dendritic spine morphogenesis / frizzled binding / axon extension / PCP/CE pathway / Wnt signalosome / WNT mediated activation of DVL / Disassembly of the destruction complex and recruitment of AXIN to the membrane / dendrite morphogenesis / neural tube development / Wnt signaling pathway, planar cell polarity pathway / clathrin-coated vesicle / regulation of postsynapse organization / neuromuscular junction development / regulation of synaptic vesicle exocytosis / heart looping / outflow tract morphogenesis / neuronal dense core vesicle / receptor clustering / synaptic vesicle exocytosis / positive regulation of excitatory postsynaptic potential / social behavior / protein localization to nucleus / lateral plasma membrane / canonical Wnt signaling pathway / prepulse inhibition / cytoplasmic microtubule organization / negative regulation of protein phosphorylation / TCF dependent signaling in response to WNT / Degradation of DVL / RHO GTPases Activate Formins / synapse organization / axon guidance / Schaffer collateral - CA1 synapse / beta-catenin binding / small GTPase binding / positive regulation of neuron projection development / regulation of protein localization / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / presynapse / growth cone / cytoplasmic vesicle / microtubule / dendritic spine / postsynaptic density / protein stabilization / intracellular signal transduction / neuron projection / positive regulation of protein phosphorylation / neuronal cell body / glutamatergic synapse / synapse / regulation of DNA-templated transcription / protein kinase binding / enzyme binding / positive regulation of transcription by RNA polymerase II / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yasukochi, S. / Numoto, N. / Tenno, N. / Tenno, T. / Ito, N. / Hiroaki, H. | ||||||
![]() | ![]() Title: Crystal structure of human Dishevelled1 PDZ domain homotrimer Authors: Yasukochi, S. / Numoto, N. / Tenno, N. / Tenno, T. / Ito, N. / Hiroaki, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 159 KB | Display | ![]() |
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PDB format | ![]() | 115.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 502.6 KB | Display | ![]() |
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Full document | ![]() | 510.9 KB | Display | |
Data in XML | ![]() | 24.2 KB | Display | |
Data in CIF | ![]() | 34.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3fy5S 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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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 10771.055 Da / Num. of mol.: 8 / Mutation: C338A,W339T Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.5 M Ammonium sulfate 0.1 M Sodium citrate tribasic dehydrate 1.0 M Lithium sulfate monohydrate 0.01 M GSH 0.01 M GSSG |
-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: Oct 17, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 25203 / % possible obs: 99.9 % / Redundancy: 5 % / Biso Wilson estimate: 58.95 Å2 / CC1/2: 0.999 / Rsym value: 0.063 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2.4→2.55 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 1.65 / Num. unique obs: 4095 / CC1/2: 0.743 / Rsym value: 0.774 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3FY5 Resolution: 2.4→26.33 Å / SU ML: 0.3832 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 32.8247
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 66.19 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→26.33 Å
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Refine LS restraints |
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LS refinement shell |
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