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- PDB-5suy: Domain-swapped dimer of human Dishevelled2 DEP domain: monoclinic... -

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Basic information

Entry
Database: PDB / ID: 5suy
TitleDomain-swapped dimer of human Dishevelled2 DEP domain: monoclinic crystal form crystallised from dimeric 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 / canonical Wnt signaling pathway / lateral plasma membrane / 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 / regulation of cell population proliferation / heart development / 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 / MOLECULAR REPLACEMENT / Resolution: 1.88 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
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2May 1, 2024Group: 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
B: Segment polarity protein dishevelled homolog DVL-2
C: Segment polarity protein dishevelled homolog DVL-2
D: Segment polarity protein dishevelled homolog DVL-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6747
Polymers43,3854
Non-polymers2883
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12200 Å2
ΔGint-132 kcal/mol
Surface area21680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.671, 60.174, 66.128
Angle α, β, γ (deg.)90.00, 117.62, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 10846.361 Da / Num. of mol.: 4 / Fragment: UNP residues 416-510
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: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.51 Å3/Da / Density % sol: 50.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES 0.1 M NaCl 0.1 M Li2SO4 22-26% PEG400 / PH range: 6.5

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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
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.202
11-H, -K, H+L20.798
ReflectionResolution: 1.88→41.98 Å / Num. obs: 34407 / % possible obs: 99 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 13.1
Reflection shellResolution: 1.88→1.96 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.963 / Mean I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: unpublished model

Resolution: 1.88→41.98 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.965 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.027 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21702 1809 5.3 %RANDOM
Rwork0.18468 ---
obs0.18641 32604 98.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.046 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å2-0 Å20.85 Å2
2--11.53 Å20 Å2
3----11.91 Å2
Refinement stepCycle: 1 / Resolution: 1.88→41.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2996 0 15 117 3128
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0193104
X-RAY DIFFRACTIONr_bond_other_d0.0020.022933
X-RAY DIFFRACTIONr_angle_refined_deg1.5911.9454204
X-RAY DIFFRACTIONr_angle_other_deg1.00236735
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2585380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.24622.374139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.74815521
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0381524
X-RAY DIFFRACTIONr_chiral_restr0.1010.2460
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023451
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02749
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4822.3981514
X-RAY DIFFRACTIONr_mcbond_other1.4822.3971513
X-RAY DIFFRACTIONr_mcangle_it2.2693.5821887
X-RAY DIFFRACTIONr_mcangle_other2.2683.5831888
X-RAY DIFFRACTIONr_scbond_it1.9332.7551590
X-RAY DIFFRACTIONr_scbond_other1.9142.7331578
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0533.982297
X-RAY DIFFRACTIONr_long_range_B_refined4.76619.6183373
X-RAY DIFFRACTIONr_long_range_B_other4.76819.5553358
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.881→1.93 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 126 -
Rwork0.233 2086 -
obs--86.41 %
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)
13.44320.33351.72370.5703-0.1681.56190.0186-0.0336-0.05430.0602-0.05360.041-0.09920.06540.03510.0671-0.00370.0020.0154-0.00040.0438-14.02288.9213-26.4713
21.78540.8632-2.93882.0742-4.760911.5819-0.02530.12190.23380.11080.0634-0.0583-0.2025-0.2245-0.03810.02520.0055-0.00990.03640.01770.0506-2.40275.6856-2.4522
32.53512.03361.33082.44381.231.9445-0.04950.16510.2372-0.0310.03480.0934-0.22280.04240.01470.0809-0.02120.00280.04070.04320.056913.93313.648412.6656
40.82140.79330.25772.03420.75252.6966-0.01320.1842-0.0886-0.05050.0897-0.08620.10650.2237-0.07660.04770.01630.02420.0767-0.00140.056412.85933.23917.7716
50.5240.19211.16830.41310.75162.9360.00760.0587-0.0025-0.0555-0.07370.039-0.07440.04350.06610.07390.017-0.00020.04010.00310.072710.9588.668820.034
62.487-0.55632.63190.2125-0.35463.4128-0.06370.0290.086-0.0227-0.0243-0.0177-0.1718-0.00360.0880.0595-0.01080.00570.02040.01220.0477-8.13789.8007-13.8011
73.3807-2.32731.77432.8476-0.83231.9472-0.0715-0.5159-0.06770.11210.14410.0103-0.0187-0.308-0.07260.02040.00430.01750.11650.01930.0394-19.70086.4865-15.9332
83.97380.74590.91092.0799-1.13042.6424-0.1001-0.4412-0.1739-0.04050.1132-0.0206-0.0254-0.0362-0.01310.01240.00640.00360.09470.02990.03-12.8514.0207-13.9109
92.7942-1.0717-1.61920.9789-0.10221.87120.00140.10530.1007-0.0780.0236-0.05550.1278-0.1445-0.02510.0879-0.00750.03160.03220.00220.0152-13.892121.032928.4746
101.1490.9319-1.71540.9845-0.23758.4626-0.00530.005-0.05640.06890.0821-0.07380.4530.4074-0.07690.09460.0524-0.020.0434-0.00320.0264-0.118921.143911.4423
112.4281-0.6056-1.63190.54190.26062.1692-0.1476-0.2627-0.02210.0243-0.0021-0.02340.20360.21330.14970.07870.02970.0290.04650.01830.031715.402720.114-10.0812
121.37-0.0796-0.67851.00380.63093.39670.002-0.12670.07530.13210.06050.0508-0.12130.1102-0.06250.05110.01090.02260.016-0.00130.018512.425525.0519-7.6389
133.24220.4152-2.3870.66690.0822.1513-0.02250.05410.0672-0.0252-0.02780.0310.1351-0.0590.05030.12260.01160.06740.0244-0.00080.052214.477820.5522-20.6685
140.10990.0397-1.11592.0441.442213.1008-0.0471-0.01040.00910.08690.2074-0.00820.58780.2912-0.16030.03790.0355-0.0170.0651-0.00820.03881.003920.8605-1.2834
151.44220.4975-1.24980.6131-0.53512.5328-0.14890.24780.00190.01520.02230.04120.312-0.24270.12670.0988-0.03890.02390.0593-0.01190.0179-14.521119.759918.0201
162.48180.25390.14541.26030.04922.9322-0.05750.18060.1499-0.0257-0.04750.0515-0.0273-0.10050.1050.04570.00470.01570.04230.01630.0256-10.059527.816213.5588
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A415 - 441
2X-RAY DIFFRACTION2A442 - 449
3X-RAY DIFFRACTION3A450 - 475
4X-RAY DIFFRACTION4A476 - 509
5X-RAY DIFFRACTION5B415 - 441
6X-RAY DIFFRACTION6B442 - 466
7X-RAY DIFFRACTION7B467 - 494
8X-RAY DIFFRACTION8B495 - 508
9X-RAY DIFFRACTION9C415 - 437
10X-RAY DIFFRACTION10C438 - 446
11X-RAY DIFFRACTION11C447 - 494
12X-RAY DIFFRACTION12C495 - 509
13X-RAY DIFFRACTION13D416 - 439
14X-RAY DIFFRACTION14D440 - 446
15X-RAY DIFFRACTION15D447 - 487
16X-RAY DIFFRACTION16D488 - 509

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