+Open data
-Basic information
Entry | Database: PDB / ID: 3ml6 | ||||||
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Title | a complex between Dishevelled2 and clathrin adaptor AP-2 | ||||||
Components | Chimeric complex between protein Dishevelled2 homolog dvl-2 and clathrin adaptor AP-2 complex subunit mu | ||||||
Keywords | PROTEIN TRANSPORT / Dishevelled / AP2 / Frizzled internalization / non-canonical Wnt signaling | ||||||
Function / homology | Function and homology information WNT mediated activation of DVL / convergent extension involved in organogenesis / PCP/CE pathway / convergent extension involved in neural plate elongation / Signaling by Hippo / 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 / convergent extension involved in neural plate elongation / Signaling by Hippo / 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 / cochlea morphogenesis / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / 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 / non-canonical Wnt signaling pathway / positive regulation of neuron projection arborization / regulation of vesicle size / RHO GTPases Activate Formins / postsynaptic neurotransmitter receptor internalization / 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 / signal sequence binding / frizzled 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 / canonical Wnt signaling pathway / lateral plasma membrane / heart morphogenesis / clathrin-coated pit / positive regulation of JUN kinase activity / neural tube closure / positive regulation of JNK cascade / intracellular protein transport / protein localization / terminal bouton / receptor internalization / Wnt signaling pathway / small GTPase binding / positive regulation of GTPase activity / : / disordered domain specific binding / protein-macromolecule adaptor activity / apical part of cell / regulation of cell population proliferation / cell cortex / heart development / cytoplasmic vesicle / postsynapse / protein-containing complex assembly / transmembrane transporter binding / cytoskeleton / nuclear body / intracellular signal transduction / positive regulation of protein phosphorylation / protein domain specific binding / synapse / lipid binding / glutamatergic synapse / regulation of DNA-templated transcription / protein kinase binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | ||||||
Authors | Yu, A. / Xing, Y. / Harrison, S.C. / Kirchhausen, T.L. | ||||||
Citation | Journal: Structure / Year: 2010 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ml6.cif.gz | 402.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ml6.ent.gz | 328.2 KB | Display | PDB format |
PDBx/mmJSON format | 3ml6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ml/3ml6 ftp://data.pdbj.org/pub/pdb/validation_reports/ml/3ml6 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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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 |
-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.) Mus musculus (house mouse), (gene. exp.) Rattus norvegicus (Norway rat) Gene: Dishevlled2, u2 / Plasmid: pPROEX-HTC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q60838, UniProt: P84092 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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 |