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- PDB-8wwr: Crystal structure of apo human dishevelled 2 (Dvl2) PDZ domain -

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Basic information

Entry
Database: PDB / ID: 8wwr
TitleCrystal structure of apo human dishevelled 2 (Dvl2) PDZ domain
ComponentsSegment polarity protein dishevelled homolog DVL-2
KeywordsSIGNALING PROTEIN / Wnt signaling
Function / homology
Function and homology information


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 / cochlea morphogenesis / segment specification / WNT5A-dependent internalization of FZD4 / non-canonical Wnt signaling pathway / positive regulation of neuron projection arborization / clathrin-coated endocytic vesicle / WNT5:FZD7-mediated leishmania damping ...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 / cochlea morphogenesis / segment specification / WNT5A-dependent internalization of FZD4 / non-canonical Wnt signaling pathway / positive regulation of neuron projection arborization / clathrin-coated endocytic vesicle / WNT5:FZD7-mediated leishmania damping / frizzled binding / PCP/CE pathway / Signaling by Hippo / WNT mediated activation of DVL / aggresome / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Wnt signaling pathway, planar cell polarity pathway / heart looping / outflow tract morphogenesis / lateral plasma membrane / canonical Wnt signaling pathway / positive regulation of JUN kinase activity / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / neural tube closure / Degradation of DVL / RHO GTPases Activate Formins / regulation of actin cytoskeleton organization / positive regulation of JNK cascade / protein localization / small GTPase binding / positive regulation of DNA-binding transcription factor activity / : / Cargo recognition for clathrin-mediated endocytosis / apical part of cell / Clathrin-mediated endocytosis / protein-macromolecule adaptor activity / heart development / regulation of cell population proliferation / cytoplasmic vesicle / nuclear body / intracellular signal transduction / positive regulation of protein phosphorylation / protein domain specific binding / regulation of DNA-templated transcription / protein kinase binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Dishevelled-2 / 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 ...Dishevelled-2 / 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-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsOmble, A. / Mahajan, S. / Kulkarni, K.A.
Funding support India, 1items
OrganizationGrant numberCountry
Council of Scientific & Industrial Research (CSIR) India
CitationJournal: Commun Biol / Year: 2024
Title: Dishevelled2 activates WGEF via its interaction with a unique internal peptide motif of the GEF.
Authors: Omble, A. / Mahajan, S. / Bhoite, A. / Kulkarni, K.
History
DepositionOct 26, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Segment polarity protein dishevelled homolog DVL-2


Theoretical massNumber of molelcules
Total (without water)10,2201
Polymers10,2201
Non-polymers00
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5410 Å2
Unit cell
Length a, b, c (Å)45.978, 45.978, 78.422
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Segment polarity protein dishevelled homolog DVL-2 / Dishevelled-2 / DSH homolog 2


Mass: 10219.759 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DVL2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: O14641
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.03 Å3/Da / Density % sol: 39.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M Tri-sodium citrate, pH 5.6 20% (v/v) Isopropanol 20%(w/v) PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Apr 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 1.75→32.51 Å / Num. obs: 9023 / % possible obs: 100 % / Observed criterion σ(F): 2 / Redundancy: 17.5 % / Biso Wilson estimate: 26.41 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Net I/σ(I): 23.3
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 15.9 % / Rmerge(I) obs: 0.731 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 482 / CC1/2: 0.915 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→32.51 Å / SU ML: 0.1947 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.0822
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2527 390 4.34 %
Rwork0.227 8594 -
obs0.2282 8984 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.78 Å2
Refinement stepCycle: LAST / Resolution: 1.75→32.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms620 0 0 20 640
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068624
X-RAY DIFFRACTIONf_angle_d1.0889841
X-RAY DIFFRACTIONf_chiral_restr0.0648106
X-RAY DIFFRACTIONf_plane_restr0.0062106
X-RAY DIFFRACTIONf_dihedral_angle_d6.626989
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.810.3322420.2705820X-RAY DIFFRACTION100
1.81-1.890.3365400.2488830X-RAY DIFFRACTION100
1.89-1.970.3074440.2209838X-RAY DIFFRACTION99.77
1.97-2.070.2939300.2406851X-RAY DIFFRACTION99.89
2.08-2.20.2921400.2459844X-RAY DIFFRACTION100
2.21-2.370.2322400.2415840X-RAY DIFFRACTION99.77
2.38-2.610.2714360.2429864X-RAY DIFFRACTION100
2.62-2.990.2642360.236867X-RAY DIFFRACTION99.89
2.99-3.770.2423460.2082882X-RAY DIFFRACTION99.89
3.77-32.510.2221360.2166958X-RAY DIFFRACTION99.7
Refinement TLS params.Method: refined / Origin x: 8.50297704862 Å / Origin y: -4.10464289136 Å / Origin z: -7.05901320309 Å
111213212223313233
T0.196783540216 Å2-0.0171060649268 Å20.0202329770353 Å2-0.150683917008 Å20.00474858660543 Å2--0.189913897259 Å2
L1.99105073791 °2-0.882701802573 °2-0.47228543118 °2-3.33716713399 °22.2516502704 °2--3.37001046908 °2
S-0.0488697121052 Å °-0.138736581778 Å °-0.0191547421282 Å °0.157535457133 Å °0.092673334289 Å °0.0705515143028 Å °0.121263225078 Å °-0.0569406016134 Å °-0.0521721485074 Å °
Refinement TLS groupSelection details: all

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