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- PDB-3pz8: Crystal structure of Dvl1-DIX(Y17D) mutant -

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Basic information

Entry
Database: PDB / ID: 3pz8
TitleCrystal structure of Dvl1-DIX(Y17D) mutant
ComponentsSegment polarity protein dishevelled homolog DVL-1
KeywordsSIGNALING PROTEIN / DIX domain / oligomerization
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 / : / postsynapse organization / cochlea morphogenesis / 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 / : / postsynapse organization / cochlea morphogenesis / Degradation of DVL / protein localization to microtubule / positive regulation of neuron projection arborization / RHO GTPases Activate Formins / presynapse assembly / collateral sprouting / neurotransmitter secretion / frizzled binding / dendritic spine morphogenesis / 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 / neuromuscular junction development / receptor clustering / heart looping / outflow tract morphogenesis / neuronal dense core vesicle / synaptic vesicle exocytosis / positive regulation of excitatory postsynaptic potential / social behavior / 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 / small GTPase binding / positive regulation of neuron projection development / beta-catenin binding / 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 / positive regulation of protein phosphorylation / axon / neuronal cell body / glutamatergic synapse / synapse / dendrite / protein kinase binding / positive regulation of transcription by RNA polymerase II / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Ribosomal Protein L25; Chain P - #130 / 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 ...Ribosomal Protein L25; Chain P - #130 / 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 / Ribosomal Protein L25; Chain P / 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 / Ubiquitin-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Segment polarity protein dishevelled homolog DVL-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.873 Å
AuthorsDan, Q.J. / Chen, L. / Zhang, Y.Y. / Liu, Y.T. / Wu, J.W.
CitationJournal: To be Published
Title: Molecular basis of WNT activation via the DIX-domain protein CCD1
Authors: Liu, Y.T. / Dan, Q.J. / Wang, J.W. / Feng, Y.G. / Chen, L. / Liang, J. / Li, Q.X. / Lin, S.C. / Wang, Z.X. / Wu, J.W.
History
DepositionDec 14, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

Downloads & links

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Assembly

Deposited unit
A: Segment polarity protein dishevelled homolog DVL-1
B: Segment polarity protein dishevelled homolog DVL-1
C: Segment polarity protein dishevelled homolog DVL-1
D: Segment polarity protein dishevelled homolog DVL-1
E: Segment polarity protein dishevelled homolog DVL-1
F: Segment polarity protein dishevelled homolog DVL-1
G: Segment polarity protein dishevelled homolog DVL-1
H: Segment polarity protein dishevelled homolog DVL-1


Theoretical massNumber of molelcules
Total (without water)95,0998
Polymers95,0998
Non-polymers00
Water73941
1
A: Segment polarity protein dishevelled homolog DVL-1


Theoretical massNumber of molelcules
Total (without water)11,8871
Polymers11,8871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Segment polarity protein dishevelled homolog DVL-1


Theoretical massNumber of molelcules
Total (without water)11,8871
Polymers11,8871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Segment polarity protein dishevelled homolog DVL-1


Theoretical massNumber of molelcules
Total (without water)11,8871
Polymers11,8871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Segment polarity protein dishevelled homolog DVL-1


Theoretical massNumber of molelcules
Total (without water)11,8871
Polymers11,8871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Segment polarity protein dishevelled homolog DVL-1


Theoretical massNumber of molelcules
Total (without water)11,8871
Polymers11,8871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Segment polarity protein dishevelled homolog DVL-1


Theoretical massNumber of molelcules
Total (without water)11,8871
Polymers11,8871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Segment polarity protein dishevelled homolog DVL-1


Theoretical massNumber of molelcules
Total (without water)11,8871
Polymers11,8871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Segment polarity protein dishevelled homolog DVL-1


Theoretical massNumber of molelcules
Total (without water)11,8871
Polymers11,8871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.687, 106.780, 265.957
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

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


Mass: 11887.325 Da / Num. of mol.: 8 / Fragment: DIX domain / Mutation: E3D, Y17D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dvl1, Dvl / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P51141
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.46 Å3/Da / Density % sol: 64.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.1M Hepes, 10% Ethylene Glycol, 0.66M Sodium Citrate, 0.3M Sodium Chloride, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.873→41.015 Å / Num. all: 30176 / Num. obs: 30176 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 85.3 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 23.1
Reflection shellResolution: 2.873→2.95 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.661 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2965 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PZ7

3pz7


Resolution: 2.873→41.015 Å / SU ML: 0.32 / σ(F): 1.33 / Phase error: 28.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2646 1521 5.04 %RANDOM
Rwork0.2298 ---
obs0.2316 30175 98.76 %-
all-30176 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 72.915 Å2 / ksol: 0.327 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.0672 Å20 Å20 Å2
2---1.2695 Å2-0 Å2
3----0.7977 Å2
Refinement stepCycle: LAST / Resolution: 2.873→41.015 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5368 0 0 41 5409
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095503
X-RAY DIFFRACTIONf_angle_d1.1937450
X-RAY DIFFRACTIONf_dihedral_angle_d20.9852008
X-RAY DIFFRACTIONf_chiral_restr0.078826
X-RAY DIFFRACTIONf_plane_restr0.004954
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8733-2.9660.43291090.35232317X-RAY DIFFRACTION88
2.966-3.0720.31931310.32112604X-RAY DIFFRACTION100
3.072-3.19490.33121280.28182609X-RAY DIFFRACTION100
3.1949-3.34030.28911590.27392589X-RAY DIFFRACTION100
3.3403-3.51630.29921330.26082598X-RAY DIFFRACTION100
3.5163-3.73640.3391540.25492614X-RAY DIFFRACTION100
3.7364-4.02470.28491320.24522636X-RAY DIFFRACTION100
4.0247-4.42930.24921410.20482638X-RAY DIFFRACTION100
4.4293-5.06920.20911500.16952629X-RAY DIFFRACTION100
5.0692-6.38280.23841500.20372649X-RAY DIFFRACTION100
6.3828-41.01880.22041340.20672771X-RAY DIFFRACTION98

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