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- PDB-6iw3: High resolution structure of Dvl2-DIX Y27W/C80S mutant -

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Entry
Database: PDB / ID: 6iw3
TitleHigh resolution structure of Dvl2-DIX Y27W/C80S mutant
ComponentsSegment polarity protein dishevelled homolog DVL-2
KeywordsSIGNALING PROTEIN / 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 / : / cochlea morphogenesis / segment specification / WNT5A-dependent internalization of FZD4 / positive regulation of neuron projection arborization / non-canonical Wnt signaling pathway / 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 / : / cochlea morphogenesis / segment specification / WNT5A-dependent internalization of FZD4 / positive regulation of neuron projection arborization / non-canonical Wnt signaling pathway / clathrin-coated endocytic vesicle / WNT5:FZD7-mediated leishmania damping / frizzled binding / PCP/CE pathway / Signaling by Hippo / WNT mediated activation of DVL / Disassembly of the destruction complex and recruitment of AXIN to the membrane / aggresome / 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 / neural tube closure / TCF dependent signaling in response to WNT / Asymmetric localization of PCP proteins / RHO GTPases Activate Formins / regulation of actin cytoskeleton organization / Degradation of DVL / positive regulation of JNK cascade / positive regulation of DNA-binding transcription factor activity / small GTPase binding / protein localization / Cargo recognition for clathrin-mediated endocytosis / apical part of cell / Clathrin-mediated endocytosis / heart development / regulation of cell population proliferation / protein-macromolecule adaptor activity / 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
Ribosomal Protein L25; Chain P - #130 / 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 ...Ribosomal Protein L25; Chain P - #130 / 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 / 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-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsYamanishi, K. / Shibata, N.
Funding support Japan, 2items
OrganizationGrant numberCountry
23121526 Japan
25121731 Japan
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2019
Title: High-resolution structure of a Y27W mutant of the Dishevelled2 DIX domain.
Authors: Yamanishi, K. / Sin, Y. / Terawaki, S.I. / Higuchi, Y. / Shibata, N.
History
DepositionDec 4, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 20, 2019Provider: 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-2


Theoretical massNumber of molelcules
Total (without water)9,3111
Polymers9,3111
Non-polymers00
Water1,06359
1
A: Segment polarity protein dishevelled homolog DVL-2
x 6


Theoretical massNumber of molelcules
Total (without water)55,8696
Polymers55,8696
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z+1/31
crystal symmetry operation3_555-x+y,-x,z+2/31
crystal symmetry operation4_555-x,-y,z+1/21
crystal symmetry operation5_555y,-x+y,z+5/61
crystal symmetry operation6_555x-y,x,z+1/61
Unit cell
Length a, b, c (Å)44.470, 44.470, 87.650
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

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


Mass: 9311.475 Da / Num. of mol.: 1 / Fragment: DIX-domain / Mutation: Y27W, C80S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DVL2 / Production host: Escherichia coli (E. coli) / References: UniProt: O14641
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.72 Å3/Da / Density % sol: 54.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% (w/v) PEG 6000, Tris-HCl pH 8.0, 200 mM lithium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: May 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. obs: 12127 / % possible obs: 100 % / Redundancy: 19.7 % / Biso Wilson estimate: 36 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.133 / Rrim(I) all: 0.136 / Net I/σ(I): 20.3
Reflection shellResolution: 1.64→1.68 Å / Redundancy: 13.9 % / Rmerge(I) obs: 2.3 / Num. unique obs: 873 / CC1/2: 0.511 / Rrim(I) all: 2.37 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WIP

4wip


Resolution: 1.64→38.5 Å / SU R Cruickshank DPI: 0.116 / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2292 1216 10.03 %
Rwork0.1998 --
obs0.2026 12118 99.88 %
Refinement stepCycle: LAST / Resolution: 1.64→38.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms649 0 0 59 708
LS refinement shellResolution: 1.64→1.702 Å
RfactorNum. reflection% reflection
Rfree0.3308 135 -
Rwork0.3174 1204 -
obs--100 %
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)
12.84264895506-3.20503597624-3.9834469447.683024055561.982328574768.2144762248-0.595981172019-0.163996168757-0.08468717150180.1575000848180.272161185990.1046739160330.5286286464070.2636610336320.2542471844770.249825695288-0.0171944583839-0.04197636464930.185124006109-0.01748492653160.29686876685717.3530849236-7.94466434839-8.36713959816
21.75866822969-2.215943723530.2102148077753.715975441470.9682945776463.50409113727-0.3286329613940.2147691157770.1692618707861.08367068993-0.3933927377281.96450988538-0.354128857836-1.403040889520.6976957282580.40366572842-0.05431077761990.05786016579560.420672038531-0.1213969733410.5550993459534.33478631966-4.6848182001-6.41530266024
32.17289427318-0.829334333123-3.002636218297.04126980239-0.4647071272358.165824528340.06029080750240.277717523177-0.506647996477-0.315927551969-0.04053841846620.3643754387160.4561828817250.480771329963-0.04323948908770.2531033914250.0223144426462-0.05143064608670.208255170669-0.04207643230480.24763401926616.2914834334-9.80716839682-11.800368423
41.12417576904-1.162184282961.901070665646.540963176950.577317154094.43707972687-0.39890367710.9446073933210.05120130171170.3026588894750.406111411467-1.364251196050.33848505641.29039610712-0.1762870203820.2294209042250.02479372747590.02961600310540.530244324935-0.01591550976240.33540246415129.4557855589-5.65733753363-8.98947289237
52.477261805672.830462586791.295988980338.821377925011.881556279781.67093928677-0.5003123615821.02838471001-0.172121761381-0.9477873093330.422023934169-0.119122741440.005188299792370.7104027617980.09210661319330.373356174342-0.04692175475090.004957114469210.3115357877430.0172544990020.24287195996121.4664949269-0.241089228526-13.6622328525
68.343192282951.986810703343.134020687462.189349374852.756896727464.8616082654-0.5264121463761.227852991680.271976185815-1.457367294231.194039003760.896318290886-1.44505388664-1.5287776367-0.5258376209780.690580004371-0.155812492314-0.05849471481410.6681420761070.1262505263030.55046259113213.39281088892.75578847039-16.9997601974
75.06568458977-2.39562927098-2.200950968573.600781572230.8573706274222.17356270148-0.308452544619-0.5811607246690.2142877057010.8490757401280.296072945473-0.115141232877-1.143310349740.4296113566210.05500532858870.4652712919930.0107772618767-0.03915637053170.226882185330.01314160876740.2478130573717.92053541872.423158508913.64471572346
84.55632043468-0.2499600557830.8206970909632.61266942498-0.7315553053445.08792839049-0.2078816192530.09124817768450.277434308135-0.2719589821610.133853521817-0.56105812008-0.2812955451250.4523748869710.07790833025980.232956317406-0.0341952179406-0.04034966668940.2263394395530.003243867671140.22892805047524.9714091957-0.24107426705-4.4972726085
94.26216757506-2.766773058671.696916148552.10254255239-1.226187339827.121366975340.01061592369010.55675823327-0.233142751502-0.465726713347-0.1550881845480.433585746272-0.156698767545-0.0151911855403-0.009371668620040.224668143785-0.000118980167237-0.04663878448770.154792013921-0.00707508166950.27574049067213.5274489199-1.38133905726-5.24727908033
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 20 )A12 - 20
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 26 )A21 - 26
3X-RAY DIFFRACTION3chain 'A' and (resid 27 through 31 )A27 - 31
4X-RAY DIFFRACTION4chain 'A' and (resid 32 through 39 )A32 - 39
5X-RAY DIFFRACTION5chain 'A' and (resid 40 through 46 )A40 - 46
6X-RAY DIFFRACTION6chain 'A' and (resid 47 through 53 )A47 - 53
7X-RAY DIFFRACTION7chain 'A' and (resid 54 through 70 )A54 - 70
8X-RAY DIFFRACTION8chain 'A' and (resid 71 through 83 )A71 - 83
9X-RAY DIFFRACTION9chain 'A' and (resid 84 through 92 )A84 - 92

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