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- PDB-6jck: Complex structure of Axin-DIX and Dvl2-DIX -

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Basic information

Entry
Database: PDB / ID: 6jck
TitleComplex structure of Axin-DIX and Dvl2-DIX
Components
  • Axin-1AXIN1
  • Segment 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 / planar cell polarity pathway involved in neural tube closure / armadillo repeat domain binding / cochlea morphogenesis / head development / segment specification / WNT5A-dependent internalization of FZD4 / cell development / dorsal/ventral axis specification ...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 / armadillo repeat domain binding / cochlea morphogenesis / head development / segment specification / WNT5A-dependent internalization of FZD4 / cell development / dorsal/ventral axis specification / non-canonical Wnt signaling pathway / positive regulation of neuron projection arborization / axial mesoderm formation / WNT5:FZD7-mediated leishmania damping / clathrin-coated endocytic vesicle / post-anal tail morphogenesis / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / epigenetic programming in the zygotic pronuclei / beta-catenin destruction complex / positive regulation of ubiquitin-dependent protein catabolic process / frizzled binding / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / PCP/CE pathway / I-SMAD binding / Wnt signalosome / 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 / nucleocytoplasmic transport / negative regulation of protein metabolic process / negative regulation of fat cell differentiation / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / heart looping / outflow tract morphogenesis / negative regulation of transcription elongation by RNA polymerase II / positive regulation of transforming growth factor beta receptor signaling pathway / activation of protein kinase activity / SMAD binding / R-SMAD binding / ubiquitin-like ligase-substrate adaptor activity / lateral plasma membrane / canonical Wnt signaling pathway / signaling adaptor activity / cytoplasmic microtubule organization / positive regulation of JUN kinase activity / positive regulation of peptidyl-threonine phosphorylation / positive regulation of protein ubiquitination / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / neural tube closure / RHO GTPases Activate Formins / cell periphery / Degradation of DVL / regulation of actin cytoskeleton organization / Degradation of AXIN / sensory perception of sound / positive regulation of JNK cascade / Degradation of beta-catenin by the destruction complex / negative regulation of canonical Wnt signaling pathway / protein localization / beta-catenin binding / small GTPase binding / protein polyubiquitination / positive regulation of DNA-binding transcription factor activity / positive regulation of protein catabolic process / : / microtubule cytoskeleton / protein-macromolecule adaptor activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / p53 binding / Cargo recognition for clathrin-mediated endocytosis / apical part of cell / Clathrin-mediated endocytosis / positive regulation of peptidyl-serine phosphorylation / regulation of cell population proliferation / heart development / cell cortex / cytoplasmic vesicle / proteasome-mediated ubiquitin-dependent protein catabolic process / protein-containing complex assembly / Estrogen-dependent gene expression / in utero embryonic development / molecular adaptor activity / nuclear body / Ub-specific processing proteases / intracellular signal transduction / positive regulation of protein phosphorylation / protein domain specific binding / negative regulation of gene expression / apoptotic process
Similarity search - Function
Ribosomal Protein L25; Chain P - #130 / Axin beta-catenin binding / Axin-1/2, tankyrase-binding domain / Axin-like / Axin beta-catenin binding motif / Axin-1 tankyrase binding domain / Dishevelled-2 / Dishevelled protein domain / Dishevelled family / Dishevelled C-terminal ...Ribosomal Protein L25; Chain P - #130 / Axin beta-catenin binding / Axin-1/2, tankyrase-binding domain / Axin-like / Axin beta-catenin binding motif / Axin-1 tankyrase binding 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 / RGS, subdomain 1/3 / 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 / Regulator of G protein signaling domain / RGS, subdomain 2 / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS domain superfamily / 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 / Axin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.09 Å
AuthorsYamanishi, K. / Shibata, N.
Funding support Japan, 2items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)23121526 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)25121731 Japan
CitationJournal: Sci.Signal. / Year: 2019
Title: A direct heterotypic interaction between the DIX domains of Dishevelled and Axin mediates signaling to beta-catenin.
Authors: Yamanishi, K. / Fiedler, M. / Terawaki, S.I. / Higuchi, Y. / Bienz, M. / Shibata, N.
History
DepositionJan 29, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 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: Axin-1
B: Segment polarity protein dishevelled homolog DVL-2


Theoretical massNumber of molelcules
Total (without water)18,6902
Polymers18,6902
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-1 kcal/mol
Surface area8880 Å2
Unit cell
Length a, b, c (Å)49.000, 56.700, 60.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Axin-1 / AXIN1 / Axis inhibition protein 1 / hAxin


Mass: 9471.836 Da / Num. of mol.: 1 / Mutation: Y760D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AXIN1, AXIN / Plasmid: pCold-GST / Production host: Escherichia coli (E. coli) / References: UniProt: O15169
#2: Protein Segment polarity protein dishevelled homolog DVL-2 / Dishevelled-2 / DSH homolog 2


Mass: 9218.350 Da / Num. of mol.: 1 / Mutation: V67A,K68A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DVL2 / Plasmid: pCold-GST / Production host: Escherichia coli (E. coli) / References: UniProt: O14641

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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: 2.23 Å3/Da / Density % sol: 44.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 25% (w/v) PEG1500, 0.1 M Malonate-Imidazole-Borate buffer pH 7.0

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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 MX300HE / Detector: CCD / Date: May 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.09→50 Å / Num. obs: 3290 / % possible obs: 97.7 % / Redundancy: 3.9 % / Biso Wilson estimate: 64.45 Å2 / CC1/2: 0.985 / Rrim(I) all: 0.266 / Net I/σ(I): 5.31
Reflection shellResolution: 3.09→3.17 Å / Redundancy: 3.69 % / Mean I/σ(I) obs: 0.94 / Num. unique obs: 231 / CC1/2: 0.575 / Rrim(I) all: 1.54 / % possible all: 95.9

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Processing

Software
NameVersionClassification
PHENIX1.14_3235refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WSP, 4WIP

1wsp

4wip


Resolution: 3.09→31.6 Å / SU ML: 0.2971 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.3644
RfactorNum. reflection% reflection
Rfree0.2899 164 5.02 %
Rwork0.2563 --
obs0.258 3269 97.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 78.08 Å2
Refinement stepCycle: LAST / Resolution: 3.09→31.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1179 0 0 0 1179
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00291203
X-RAY DIFFRACTIONf_angle_d0.73161620
X-RAY DIFFRACTIONf_chiral_restr0.048179
X-RAY DIFFRACTIONf_plane_restr0.003204
X-RAY DIFFRACTIONf_dihedral_angle_d15.6874722
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.09-3.290.6192270.3135500X-RAY DIFFRACTION96.52
3.29-3.540.4581250.264515X-RAY DIFFRACTION98.54
3.54-3.890.2495270.2865497X-RAY DIFFRACTION98.31
3.89-4.460.2216270.2389520X-RAY DIFFRACTION98.56
4.46-5.610.2943280.2151518X-RAY DIFFRACTION97.5
5.61-31.60.2286300.2651555X-RAY DIFFRACTION96.69
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)
17.157335307470.001870522866871.533346888962.382511709432.187105762656.92825970555-0.170397791723-0.3196468841950.2589611113940.19208771580.2973203278960.1041956934720.287876619326-0.476465489174-0.185216172435-0.357714920902-0.1120195558070.02803800830180.213527879235-0.0348867434061.0241254628654.592186539660.519173139631.6342310045
23.69104897258-2.721148144170.2664841595534.20957377596-0.1185889255112.7722915481-0.0189443020239-0.456624044869-0.8460590498410.3345124428640.267864765128-0.001969962029980.3538433246970.561482551227-0.0795589611354-0.09543935348580.1735527424240.001845163328410.2531877309460.1140353338760.43901896472764.799936925354.856661031236.4558906347
31.996291296991.732836011610.8684185429595.533005905891.299725237833.34383477918-0.1659583045550.282217989829-0.145942195725-0.5617021607580.22585287823-0.104367832210.146836334431-0.218712999365-0.09365520016550.128312675568-0.0514434044741-0.09864768906030.29730511264-0.104203643860.48622962651460.524057503455.45401031823.7538203908
41.694889317110.03282725558110.8231855517655.782814940652.307103972773.84085748647-0.227978440748-0.03527674824480.0419752440023-0.4363973762540.456541188112-0.539942097674-0.6692970338320.4604618581480.1039091313950.270524836532-0.211331836283-0.1673085118890.482733654074-0.3193270028840.25252929861567.744103856172.073446221723.2841237115
54.079576024930.692126151738-0.2340957289670.7406467607460.05765530292041.49157414305-0.154067592364-0.332660492915-0.1072479611110.143903188156-0.1092655924130.00253573968789-0.09959140282030.2673151349-0.555187331945-0.136036140352-0.02002363153450.1774129321660.34985778109-0.1285754206461.1280758414567.058188904560.90918218228.2472221245
68.153359249382.04225530345-0.7427611629655.74761288971.17638221228.760312081310.05348455703030.8195554471480.174287628999-0.1797990247750.1518434381710.5615515864050.105227951253-0.564529557916-0.1398281951570.100110557404-0.1124346131330.02112470570230.2198210154270.1319240877210.63667387977157.176681915961.070816778822.1057703481
75.184724947511.12663429587-3.238875295441.476705323692.319395652179.46008341697-0.0129676411120.0496886635087-0.20468109551-1.44663400925-0.314782072066-0.164224290642-1.151684374980.1478254603390.06925502454180.569538840421-0.0123356465035-0.1980448883930.3455930192710.1090409079081.3053443698166.48683052570.897806934814.2490617749
84.37131688652-1.36957694836-1.812213053751.41258440123-1.395094580464.666815494030.7018573554260.5141989234020.142001760648-1.47038153099-0.8109908203420.572001584862-1.74270661585-1.199806189030.01697335296150.6812603101340.252526296188-0.1486582728790.46726998898-0.298002977191.2260047978155.892170809874.599955165119.4756203933
95.357345216753.93957285769-1.573066441185.409914537391.287709194896.12096647376-0.288343886495-0.0579516943539-0.654956974687-0.561805036511-0.0680145887178-0.0693026731807-0.2779348828580.5099079738710.2592813677750.329480423209-0.2188531913460.2005447170670.146202928677-0.03646165937890.77442103629467.037039160567.08040045615.7616103389
101.8189176435-4.14530520603-0.9989676886599.649561276813.155607367965.851242631290.06296969756920.526436386404-0.174715364763-1.584635656090.342816621051-1.02108225359-1.448023105860.656291286991-0.5443839509811.74419487953-0.2889907128350.6389033184920.669984624979-0.3259403125791.197207909275.516894338667.52800191135.10049459004
112.87873809716-0.29651986232-1.30971586434.59394474-3.887248338684.217119248030.1300552636881.63088847404-0.643416114447-2.10451894388-0.6866427518840.0234182452304-0.306275582562-1.154074925280.6242962289380.9577990056680.282849884242-0.2357155847490.908196737348-0.2342539252550.70220263698864.658886471865.31782431885.62794771728
123.229957271810.335175153311-1.709132002313.97966729452-4.780077007266.321358100950.3823459536592.16873300968-0.434560190445-2.15335457945-0.3379255621881.37678440192-0.793263755623-1.742889469090.00360483699641.765493829020.819816330616-0.1570088171741.8382234037-0.3439239819441.1318017508757.617922753169.89798501455.95490291943
134.82661439737-1.30787656917-3.533800576967.79364369717-2.497073685014.18804268130.4508296730311.117792080010.192725195457-1.36670552671-0.97844504163-0.434918873663-1.66502231436-0.774769192730.280492273061.537944238180.341891003858-0.1863036731930.8605676543920.03977847221030.95906883789167.37333045775.27966115947.27746372246
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 745 through 761 )
2X-RAY DIFFRACTION2chain 'A' and (resid 762 through 770 )
3X-RAY DIFFRACTION3chain 'A' and (resid 771 through 790 )
4X-RAY DIFFRACTION4chain 'A' and (resid 791 through 803 )
5X-RAY DIFFRACTION5chain 'A' and (resid 804 through 816 )
6X-RAY DIFFRACTION6chain 'A' and (resid 817 through 826 )
7X-RAY DIFFRACTION7chain 'B' and (resid 13 through 20 )
8X-RAY DIFFRACTION8chain 'B' and (resid 21 through 26 )
9X-RAY DIFFRACTION9chain 'B' and (resid 27 through 31 )
10X-RAY DIFFRACTION10chain 'B' and (resid 32 through 39 )
11X-RAY DIFFRACTION11chain 'B' and (resid 40 through 47 )
12X-RAY DIFFRACTION12chain 'B' and (resid 48 through 57 )
13X-RAY DIFFRACTION13chain 'B' and (resid 58 through 91 )

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