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- PDB-1fsh: STRUCTURAL BASIS OF THE RECOGNITION OF THE DISHEVELLED DEP DOMAIN... -

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Basic information

Entry
Database: PDB / ID: 1fsh
TitleSTRUCTURAL BASIS OF THE RECOGNITION OF THE DISHEVELLED DEP DOMAIN IN THE WNT SIGNALING PATHWAY
ComponentsDISHEVELLED-1
KeywordsSIGNALING PROTEIN / three-helix bundle / beta-arm / DISHEVELLED-1 / SEGMENT POLARITY PROTEIN DISHEVELLED HOMOLOG DVL-1
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 / protein localization to microtubule / positive regulation of neuron projection arborization / RHO GTPases Activate Formins / presynapse assembly / collateral sprouting / 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 / heart looping / outflow tract morphogenesis / neuronal dense core vesicle / receptor clustering / synaptic vesicle exocytosis / social behavior / positive regulation of excitatory postsynaptic potential / protein localization to nucleus / lateral plasma membrane / canonical Wnt signaling pathway / prepulse inhibition / cytoplasmic microtubule organization / axonogenesis / negative regulation of protein phosphorylation / axon guidance / synapse organization / regulation of protein phosphorylation / Schaffer collateral - CA1 synapse / small GTPase binding / beta-catenin binding / Wnt signaling pathway / positive regulation of neuron projection development / regulation of protein localization / microtubule cytoskeleton / 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 / axon / neuronal cell body / glutamatergic synapse / synapse / dendrite / 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 / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Ubiquitin-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
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. / Zheng, J.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: Structural basis of the recognition of the dishevelled DEP domain in the Wnt signaling pathway.
Authors: Wong, H.C. / Mao, J. / Nguyen, J.T. / Srinivas, S. / Zhang, W. / Liu, B. / Li, L. / Wu, D. / Zheng, J.
History
DepositionSep 8, 2000Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 8, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DISHEVELLED-1


Theoretical massNumber of molelcules
Total (without water)11,9351
Polymers11,9351
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 1000target function
RepresentativeModel #1lowest target function

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Components

#1: Protein DISHEVELLED-1 /


Mass: 11934.700 Da / Num. of mol.: 1 / Fragment: DEP DOMAIN (RESIDUES 391-495)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PQE31 / Production host: Escherichia coli (E. coli) / 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
122HNHA
1323D 15N-separated NOESY
1433D 15N-separated NOESY
1522D NOESY
164HMQC
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8-1.5mM DEP, 15N and 13C labeled, 100mM phosphate buffer (pH 6.8), 0.1mM NaN3, 3mM DTT90% H2O/10% D2O
20.8-1.5mM DEP, 15N labeled, 100mM phosphate buffer (pH 6.8), 0.1mM NaN3, 3mM DTT90% H2O/10% D2O
30.8-1.5mM DEP, valine selective 15N labeled, 100mM phosphate buffer (pH 6.8), 0.1mM NaN3, 3mM DTT90% H2O/10% D2O
40.8-1.5mM DEP, 15N labeled, 100mM phosphate buffer (pH 6.8), 0.1mM NaN3, 3mM DTT100% D2O
Sample conditionsIonic strength: 0.1 / pH: 6.8 / Pressure: ambient / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guntert, P.refinement
Felix98Molecular Simulations, Inc.processing
XEASY1.3.13Xia, T.-H.data analysis
DYANA1.5Guntert, P.structure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: The structural calculations are based on 2009 NOE distance restraints, 54 hydrogen-bond distance restraints, and 40 dihedral angle restraints
NMR representativeSelection criteria: lowest target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 1000 / Conformers submitted total number: 20

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