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- PDB-1mc7: Solution Structure of mDvl1 PDZ domain -

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Basic information

Entry
Database: PDB / ID: 1mc7
TitleSolution Structure of mDvl1 PDZ domain
ComponentsSegment polarity protein dishevelled homolog DVL-1
KeywordsSIGNALING PROTEIN / PDZ Domain / 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 / Disassembly of the destruction complex and recruitment of AXIN to the membrane / planar cell polarity pathway involved in neural tube closure / skeletal muscle acetylcholine-gated channel clustering / cochlea morphogenesis / postsynapse organization / Degradation of DVL ...WNT mediated activation of DVL / convergent extension involved in organogenesis / PCP/CE pathway / convergent extension involved in neural plate elongation / Disassembly of the destruction complex and recruitment of AXIN to the membrane / planar cell polarity pathway involved in neural tube closure / skeletal muscle acetylcholine-gated channel clustering / cochlea morphogenesis / postsynapse organization / Degradation of DVL / positive regulation of neuron projection arborization / RHO GTPases Activate Formins / protein localization to microtubule / collateral sprouting / presynapse assembly / neurotransmitter secretion / dendritic spine morphogenesis / frizzled binding / axon extension / Wnt signalosome / dendrite morphogenesis / Wnt signaling pathway, planar cell polarity pathway / regulation of postsynapse organization / clathrin-coated vesicle / regulation of synaptic vesicle exocytosis / neuromuscular junction development / receptor clustering / heart looping / neuronal dense core vesicle / outflow tract morphogenesis / synaptic vesicle exocytosis / social behavior / positive regulation of excitatory postsynaptic potential / protein localization to nucleus / canonical Wnt signaling pathway / lateral plasma membrane / prepulse inhibition / cytoplasmic microtubule organization / axonogenesis / negative regulation of protein phosphorylation / axon guidance / synapse organization / regulation of protein phosphorylation / Schaffer collateral - CA1 synapse / beta-catenin binding / Wnt signaling pathway / small GTPase binding / positive regulation of neuron projection development / microtubule cytoskeleton / 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 / neuron projection / intracellular signal transduction / positive regulation of protein phosphorylation / axon / neuronal cell body / dendrite / synapse / glutamatergic synapse / protein kinase binding / enzyme binding / positive regulation of transcription by RNA polymerase II / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Dishevelled protein domain / Dishevelled family / Dishevelled C-terminal / Dishevelled specific domain / Segment polarity protein dishevelled (Dsh) C terminal / Dishevelled-related protein / DIX domain / DIX domain superfamily / DIX domain / DIX domain profile. ...Dishevelled protein domain / Dishevelled family / Dishevelled C-terminal / Dishevelled specific domain / Segment polarity protein dishevelled (Dsh) C terminal / Dishevelled-related protein / DIX domain / DIX domain superfamily / DIX domain / DIX domain profile. / Domain present in Dishevelled and axin / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Ubiquitin-like domain superfamily / Winged helix DNA-binding domain superfamily / Roll / Winged helix-like DNA-binding domain superfamily / Mainly Beta
Similarity search - Domain/homology
Segment polarity protein dishevelled homolog DVL-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsWong, H.-C. / Bourdelas, A. / Shao, Y. / Wu, D. / Shi, D.L. / Zheng, J.
CitationJournal: Mol.Cell / Year: 2003
Title: Direct binding of the PDZ domain of Dishevelled to a conserved internal sequence in the C-terminal region of Frizzled
Authors: Wong, H.-C. / Bourdelas, A. / Krauss, A. / Lee, H.-J. / Shao, Y. / Wu, D. / Mlodzik, M. / Shi, D.-L. / Zheng, J.
History
DepositionAug 5, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Segment polarity protein dishevelled homolog DVL-1


Theoretical massNumber of molelcules
Total (without water)10,2041
Polymers10,2041
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 320target function
RepresentativeModel #1fewest violations

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Components

#1: Protein Segment polarity protein dishevelled homolog DVL-1 / Dishevelled-1 / DSH homolog 1


Mass: 10204.449 Da / Num. of mol.: 1 / Fragment: PDZ domain / Mutation: C88A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL-21 / References: UniProt: P51141

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: 1mM mDvl1 PDZ domain U-15N, 13C, 100mM phosphate buffer pH 7.5, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 7.5 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
DYANAGUNTERTstructure solution
NMRPipeprocessing
XEASYdata analysis
DYANAGUNTERTrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: the structures are based on a total of 1190 restraints: 1124 are NOE-derived distance constraints, 44 are dihedral angle restraints and 22 are distance restraints from hydrogen bonds.
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 320 / Conformers submitted total number: 20

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