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Open data
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Basic information
Entry | Database: PDB / ID: 3ml6 | ||||||
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Title | a complex between Dishevelled2 and clathrin adaptor AP-2 | ||||||
![]() | Chimeric complex between protein Dishevelled2 homolog dvl-2 and clathrin adaptor AP-2 complex subunit mu | ||||||
![]() | PROTEIN TRANSPORT / Dishevelled / AP2 / Frizzled internalization / non-canonical Wnt signaling | ||||||
Function / homology | ![]() WNT mediated activation of DVL / convergent extension involved in organogenesis / PCP/CE pathway / Signaling by Hippo / convergent extension involved in neural plate elongation / Disassembly of the destruction complex and recruitment of AXIN to the membrane / segmentation / planar cell polarity pathway involved in neural tube closure / Gap junction degradation / Formation of annular gap junctions ...WNT mediated activation of DVL / convergent extension involved in organogenesis / PCP/CE pathway / Signaling by Hippo / convergent extension involved in neural plate elongation / Disassembly of the destruction complex and recruitment of AXIN to the membrane / segmentation / planar cell polarity pathway involved in neural tube closure / Gap junction degradation / Formation of annular gap junctions / Asymmetric localization of PCP proteins / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / cochlea morphogenesis / LDL clearance / WNT5A-dependent internalization of FZD4 / VLDLR internalisation and degradation / Retrograde neurotrophin signalling / Degradation of DVL / segment specification / WNT5A-dependent internalization of FZD4 / extrinsic component of presynaptic endocytic zone membrane / MHC class II antigen presentation / AP-2 adaptor complex / positive regulation of neuron projection arborization / regulation of vesicle size / postsynaptic neurotransmitter receptor internalization / RHO GTPases Activate Formins / Recycling pathway of L1 / Cargo recognition for clathrin-mediated endocytosis / Cargo recognition for clathrin-mediated endocytosis / positive regulation of synaptic vesicle endocytosis / Clathrin-mediated endocytosis / clathrin adaptor activity / Clathrin-mediated endocytosis / vesicle budding from membrane / clathrin-dependent endocytosis / frizzled binding / signal sequence binding / aggresome / negative regulation of protein localization to plasma membrane / Wnt signaling pathway, planar cell polarity pathway / clathrin-coated vesicle / low-density lipoprotein particle receptor binding / heart looping / outflow tract morphogenesis / Trafficking of GluR2-containing AMPA receptors / positive regulation of receptor internalization / synaptic vesicle endocytosis / lateral plasma membrane / canonical Wnt signaling pathway / heart morphogenesis / clathrin-coated pit / positive regulation of JUN kinase activity / positive regulation of GTPase activity / neural tube closure / positive regulation of JNK cascade / intracellular protein transport / protein localization / receptor internalization / terminal bouton / Wnt signaling pathway / small GTPase binding / : / disordered domain specific binding / apical part of cell / protein-macromolecule adaptor activity / heart development / regulation of cell population proliferation / cell cortex / cytoplasmic vesicle / postsynapse / protein-containing complex assembly / transmembrane transporter binding / cytoskeleton / nuclear body / intracellular signal transduction / protein domain specific binding / glutamatergic synapse / lipid binding / synapse / protein kinase binding / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yu, A. / Xing, Y. / Harrison, S.C. / Kirchhausen, T.L. | ||||||
![]() | ![]() Title: Structural analysis of the interaction between Dishevelled2 and clathrin AP-2 adaptor, a critical step in noncanonical Wnt signaling. Authors: Yu, A. / Xing, Y. / Harrison, S.C. / Kirchhausen, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 402.1 KB | Display | ![]() |
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PDB format | ![]() | 328.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 511.4 KB | Display | ![]() |
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Full document | ![]() | 654.5 KB | Display | |
Data in XML | ![]() | 89.3 KB | Display | |
Data in CIF | ![]() | 118 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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5 | ![]()
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6 | ![]()
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Unit cell |
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Details | none |
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Components
#1: Protein | Mass: 43403.367 Da / Num. of mol.: 6 Fragment: PROTEIN Dishevelled2 (UNP RESIDUES 417-510), AP-2 COMPLEX 2 MU SUBUNIT (UNP RESIDUES 170-435) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() Gene: Dishevlled2, u2 / Plasmid: pPROEX-HTC / Production host: ![]() ![]() Sequence details | THE STRUCTURE IS REPRESENTATIVE OF A CHIMERIC PROTEIN BETWEEN DISHEVLLED2 AND CLATHRIN ADAPTOR AP-2 ...THE STRUCTURE IS REPRESENTA | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4 Å3/Da / Density % sol: 69.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.7 M K/Na tartrate, 0.1 M sodium citrate, pH 5.5, 10 mM DTT, 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 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→100 Å / Num. all: 51791 / Num. obs: 51429 / % possible obs: 99.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Rmerge(I) obs: 0.112 / Rsym value: 0.112 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 3.5→3.56 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.774 / Mean I/σ(I) obs: 1.5 / Num. unique all: 2485 / Rsym value: 0.774 / % possible all: 97 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1BW8, 1FSH Resolution: 3.5→49.07 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 5714272.84 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 66.0607 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 117.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.5→49.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.5→3.72 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: protein_rep.param / Topol file: protein.top |