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- PDB-5suz: Domain-swapped dimer of human Dishevelled2 DEP domain: C-centered... -

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Basic information

Entry
Database: PDB / ID: 5suz
TitleDomain-swapped dimer of human Dishevelled2 DEP domain: C-centered monoclinic crystal form crystallised from monomeric fraction
ComponentsSegment polarity protein dishevelled homolog DVL-2
KeywordsSIGNALING PROTEIN / Dishevelled / DEP domain / WNT signalling
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 / WNT5:FZD7-mediated leishmania damping / clathrin-coated endocytic vesicle ...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 / WNT5:FZD7-mediated leishmania damping / clathrin-coated endocytic vesicle / 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 / RHO GTPases Activate Formins / Degradation of DVL / regulation of actin cytoskeleton organization / positive regulation of JNK cascade / protein localization / small GTPase binding / positive regulation of DNA-binding transcription factor activity / : / protein-macromolecule adaptor activity / Cargo recognition for clathrin-mediated endocytosis / apical part of cell / Clathrin-mediated endocytosis / 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 / cytosol / cytoplasm
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 / SAD / Resolution: 1.84 Å
AuthorsRenko, M. / Gammons, M.V. / Bienz, M.
CitationJournal: Mol.Cell / Year: 2016
Title: Wnt Signalosome Assembly by DEP Domain Swapping of Dishevelled.
Authors: Gammons, M.V. / Renko, M. / Johnson, C.M. / Rutherford, T.J. / Bienz, M.
History
DepositionAug 4, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release

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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-2
B: Segment polarity protein dishevelled homolog DVL-2


Theoretical massNumber of molelcules
Total (without water)21,6862
Polymers21,6862
Non-polymers00
Water1,47782
1
A: Segment polarity protein dishevelled homolog DVL-2
B: Segment polarity protein dishevelled homolog DVL-2

A: Segment polarity protein dishevelled homolog DVL-2
B: Segment polarity protein dishevelled homolog DVL-2


Theoretical massNumber of molelcules
Total (without water)43,3724
Polymers43,3724
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area13190 Å2
ΔGint-122 kcal/mol
Surface area20540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.785, 59.601, 30.322
Angle α, β, γ (deg.)90.000, 93.640, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 10842.916 Da / Num. of mol.: 2 / Fragment: UNP residues 416-509
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DVL2 / Plasmid: pETM-41 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O14641
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.45 Å3/Da / Density % sol: 49.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES, pH=6.5 0.2 M CaCl2 23% PEG350 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.84→32.7 Å / Num. obs: 17446 / % possible obs: 92 % / Redundancy: 13.7 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 16.1
Reflection shellResolution: 1.84→1.91 Å / Redundancy: 13.6 % / Rmerge(I) obs: 2.416 / Mean I/σ(I) obs: 0.98 / Num. unique all: 1733

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
Cootmodel building
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
Aimlessdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.84→32.7 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 11.932 / SU ML: 0.164 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.168 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2627 852 5 %RANDOM
Rwork0.2173 ---
obs0.2195 16251 94.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.68 Å2 / Biso mean: 40.485 Å2 / Biso min: 25.09 Å2
Baniso -1Baniso -2Baniso -3
1--3.08 Å2-0 Å20.06 Å2
2--2.23 Å20 Å2
3---0.83 Å2
Refinement stepCycle: final / Resolution: 1.84→32.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1504 0 0 82 1586
Biso mean---42.57 -
Num. residues----190
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191558
X-RAY DIFFRACTIONr_bond_other_d0.0010.021488
X-RAY DIFFRACTIONr_angle_refined_deg1.5551.9622110
X-RAY DIFFRACTIONr_angle_other_deg0.97433420
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6125194
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.49322.35368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.56615244
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5751512
X-RAY DIFFRACTIONr_chiral_restr0.0890.2232
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021735
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02373
X-RAY DIFFRACTIONr_mcbond_it1.4182.88764
X-RAY DIFFRACTIONr_mcbond_other1.4142.879763
X-RAY DIFFRACTIONr_mcangle_it2.3594.305953
LS refinement shellResolution: 1.844→1.891 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 79 -
Rwork0.314 1215 -
all-1294 -
obs--95.43 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.1823-2.20360.07432.2704-0.14690.2658-0.01130.11570.0290.0549-0.0391-0.0557-0.0129-0.03220.05040.06270.0162-0.07090.1142-0.01080.096236.99381.082421.2937
24.2401-3.279-1.58284.57132.80531.81960.10240.3770.2322-0.204-0.1354-0.0108-0.1302-0.01570.0330.05460.0019-0.03880.08720.06250.075771.2972-16.563519.092
31.3543-1.3475-1.08852.79981.91993.4496-0.1333-0.0018-0.27220.11410.0310.38450.235-0.05860.10240.0692-0.0274-0.02690.0510.00980.123270.5227-27.266621.4363
44.54480.5919-0.27321.17570.59652.0153-0.0496-0.3387-0.1220.1003-0.02010.19370.1954-0.07720.06970.0608-0.0252-0.01680.07140.04210.078867.0453-20.081426.3429
52.7147-3.1220.20353.6022-0.23550.43350.06090.03480.0266-0.0833-0.0088-0.01210.0461-0.0466-0.05210.0597-0.015-0.05770.09890.02750.066580.1824-20.726320.7221
63.8537-3.46071.01333.1331-0.92830.28530.13580.18580.1838-0.156-0.139-0.15880.0610.02010.00320.06470.0012-0.03080.10140.00970.144646.3545-2.024920.1194
71.3189-2.29980.10614.1622-0.72632.0284-0.0379-0.01260.51350.07730.0398-0.8637-0.1211-0.0775-0.00190.0315-0.006-0.04950.01340.00970.268343.220910.078621.9468
83.5669-2.01261.7011.9521-1.53091.278-0.25470.01350.41550.30980.0059-0.4412-0.17530.00180.24880.1173-0.007-0.14460.0461-0.03410.222746.68512.87826.8765
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A415 - 445
2X-RAY DIFFRACTION2A446 - 466
3X-RAY DIFFRACTION3A467 - 492
4X-RAY DIFFRACTION4A493 - 509
5X-RAY DIFFRACTION5B415 - 441
6X-RAY DIFFRACTION6B442 - 466
7X-RAY DIFFRACTION7B467 - 492
8X-RAY DIFFRACTION8B493 - 509

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