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- PDB-6lca: Crystal structure of human Dishevelled1 PDZ domain homotrimer -

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Basic information

Entry
Database: PDB / ID: 6lca
TitleCrystal structure of human Dishevelled1 PDZ domain homotrimer
ComponentsSegment polarity protein dishevelled homolog DVL-1
KeywordsSIGNALING PROTEIN / Wnt signaling pathway / Developmental protein / PROTEIN BINDING / Dvl
Function / homology
Function and homology information


positive regulation of protein localization to presynapse / Negative regulation of TCF-dependent signaling by DVL-interacting proteins / convergent extension involved in neural plate elongation / planar cell polarity pathway involved in neural tube closure / skeletal muscle acetylcholine-gated channel clustering / cochlea morphogenesis / non-canonical Wnt signaling pathway / positive regulation of neuron projection arborization / protein localization to microtubule / collateral sprouting ...positive regulation of protein localization to presynapse / Negative regulation of TCF-dependent signaling by DVL-interacting proteins / convergent extension involved in neural plate elongation / planar cell polarity pathway involved in neural tube closure / skeletal muscle acetylcholine-gated channel clustering / cochlea morphogenesis / non-canonical Wnt signaling pathway / positive regulation of neuron projection arborization / protein localization to microtubule / collateral sprouting / presynapse assembly / WNT5:FZD7-mediated leishmania damping / neurotransmitter secretion / dendritic spine morphogenesis / frizzled binding / axon extension / PCP/CE pathway / Wnt signalosome / WNT mediated activation of DVL / Disassembly of the destruction complex and recruitment of AXIN to the membrane / dendrite morphogenesis / Wnt signaling pathway, planar cell polarity pathway / neural tube development / 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 / negative regulation of protein phosphorylation / TCF dependent signaling in response to WNT / RHO GTPases Activate Formins / axon guidance / Degradation of DVL / synapse organization / Schaffer collateral - CA1 synapse / beta-catenin binding / small GTPase binding / positive regulation of neuron projection development / 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 / neuronal cell body / synapse / glutamatergic synapse / regulation of DNA-templated transcription / protein kinase binding / enzyme binding / positive regulation of transcription by RNA polymerase II / identical protein binding / 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 / Ubiquitin-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Segment polarity protein dishevelled homolog DVL-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsYasukochi, S. / Numoto, N. / Tenno, N. / Tenno, T. / Ito, N. / Hiroaki, H.
CitationJournal: To Be Published
Title: Crystal structure of human Dishevelled1 PDZ domain homotrimer
Authors: Yasukochi, S. / Numoto, N. / Tenno, N. / Tenno, T. / Ito, N. / Hiroaki, H.
History
DepositionNov 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,93716
Polymers86,1688
Non-polymers7698
Water39622
1
A: Segment polarity protein dishevelled homolog DVL-1
B: Segment polarity protein dishevelled homolog DVL-1
C: Segment polarity protein dishevelled homolog DVL-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6016
Polymers32,3133
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Segment polarity protein dishevelled homolog DVL-1
E: Segment polarity protein dishevelled homolog DVL-1
G: Segment polarity protein dishevelled homolog DVL-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6016
Polymers32,3133
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
F: Segment polarity protein dishevelled homolog DVL-1
hetero molecules

F: Segment polarity protein dishevelled homolog DVL-1
hetero molecules

F: Segment polarity protein dishevelled homolog DVL-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6016
Polymers32,3133
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-y+2,x-y,z1
crystal symmetry operation3_775-x+y+2,-x+2,z1
4
H: Segment polarity protein dishevelled homolog DVL-1
hetero molecules

H: Segment polarity protein dishevelled homolog DVL-1
hetero molecules

H: Segment polarity protein dishevelled homolog DVL-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6016
Polymers32,3133
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
Unit cell
Length a, b, c (Å)147.923, 147.923, 78.999
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

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Components

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


Mass: 10771.055 Da / Num. of mol.: 8 / Mutation: C338A,W339T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DVL1 / Plasmid: pGEX-6P3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O14640
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.93 Å3/Da / Density % sol: 36.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.5 M Ammonium sulfate 0.1 M Sodium citrate tribasic dehydrate 1.0 M Lithium sulfate monohydrate 0.01 M GSH 0.01 M GSSG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 25203 / % possible obs: 99.9 % / Redundancy: 5 % / Biso Wilson estimate: 58.95 Å2 / CC1/2: 0.999 / Rsym value: 0.063 / Net I/σ(I): 14.3
Reflection shellResolution: 2.4→2.55 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 1.65 / Num. unique obs: 4095 / CC1/2: 0.743 / Rsym value: 0.774 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FY5

3fy5


Resolution: 2.4→26.33 Å / SU ML: 0.3832 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 32.8247
RfactorNum. reflection% reflection
Rfree0.2727 1265 5.02 %
Rwork0.2449 --
obs0.2464 25181 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 66.19 Å2
Refinement stepCycle: LAST / Resolution: 2.4→26.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5368 0 40 22 5430
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00245446
X-RAY DIFFRACTIONf_angle_d0.5367357
X-RAY DIFFRACTIONf_chiral_restr0.0473868
X-RAY DIFFRACTIONf_plane_restr0.0027973
X-RAY DIFFRACTIONf_dihedral_angle_d15.36383263
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.50.34421380.2712681X-RAY DIFFRACTION99.75
2.5-2.610.31971420.27612649X-RAY DIFFRACTION99.96
2.61-2.750.32291390.28072638X-RAY DIFFRACTION100
2.75-2.920.38781400.29872672X-RAY DIFFRACTION100
2.92-3.140.32671400.2952661X-RAY DIFFRACTION99.96
3.14-3.460.3441430.28272665X-RAY DIFFRACTION100
3.46-3.960.30631390.25852640X-RAY DIFFRACTION100
3.96-4.980.24331410.21122669X-RAY DIFFRACTION99.96
4.98-26.330.19651430.21252641X-RAY DIFFRACTION99.61

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