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- PDB-2mx6: Complex structure of Dvl PDZ domain with ligand -

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Basic information

Entry
Database: PDB / ID: 2mx6
TitleComplex structure of Dvl PDZ domain with ligand
Components
  • (PHQ)WV peptide
  • Segment polarity protein dishevelled homolog DVL-1
KeywordsPEPTIDE BINDING PROTEIN / PDZ / Dvl
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 / 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 / skeletal muscle acetylcholine-gated channel clustering / : / cochlea morphogenesis / postsynapse organization / Degradation of DVL / protein localization to microtubule / RHO GTPases Activate Formins / positive regulation of neuron projection arborization / presynapse assembly / collateral sprouting / neurotransmitter secretion / dendritic spine morphogenesis / frizzled binding / axon extension / Wnt signalosome / dendrite morphogenesis / Wnt signaling pathway, planar cell polarity pathway / clathrin-coated vesicle / regulation of postsynapse organization / regulation of synaptic vesicle exocytosis / receptor clustering / neuromuscular junction development / heart looping / neuronal dense core vesicle / outflow tract morphogenesis / 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 / Wnt signaling pathway / beta-catenin binding / positive regulation of neuron projection development / small GTPase binding / microtubule cytoskeleton / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / regulation of protein localization / presynapse / growth cone / cytoplasmic vesicle / microtubule / dendritic spine / postsynaptic density / protein stabilization / intracellular signal transduction / positive regulation of protein phosphorylation / axon / neuronal cell body / glutamatergic synapse / dendrite / synapse / protein kinase 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 / Roll / Winged helix DNA-binding domain superfamily / 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)
synthetic construct (others)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsZhang, X. / Zheng, J.J.
CitationJournal: To be Published
Title: Protein-ligand interaction decoded by NMR chemical shift analysis
Authors: Zhang, X. / Zheng, J.J.
History
DepositionDec 15, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_spectrometer / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag

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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
B: (PHQ)WV peptide


Theoretical massNumber of molelcules
Total (without water)10,0892
Polymers10,0892
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 9632.888 Da / Num. of mol.: 1 / Fragment: UNP residues 248-337
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dvl1, Dvl / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: P51141
#2: Protein/peptide (PHQ)WV peptide


Mass: 455.934 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-13C NOESY
1212D 1H-15N HSQC
1313D HNCA
1413D HN(CA)CB
1512D 1H-1H TOCSY

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Sample preparation

DetailsContents: 1 mM [U-100% 13C; U-100% 15N] protein, 10 mM peptide, 100 mM potassium phosphate, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMprotein-1[U-100% 13C; U-100% 15N]1
10 mMpeptide-21
100 mMpotassium phosphate-31
Sample conditionsIonic strength: 0.1 / pH: 7.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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