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- PDB-8s6a: X-ray structure of Dishevelled 3 PDZ domain in a complex with a c... -

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Basic information

Entry
Database: PDB / ID: 8s6a
TitleX-ray structure of Dishevelled 3 PDZ domain in a complex with a class III peptide ligand
Components
  • C8 peptide
  • Segment polarity protein dishevelled homolog DVL-3
KeywordsSIGNALING PROTEIN / Dishevelled / Wnt signalling
Function / homology
Function and homology information


Negative regulation of TCF-dependent signaling by DVL-interacting proteins / positive regulation of neuron projection arborization / non-canonical Wnt signaling pathway / WNT5:FZD7-mediated leishmania damping / frizzled binding / PCP/CE pathway / WNT mediated activation of DVL / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Wnt signaling pathway, planar cell polarity pathway / canonical Wnt signaling pathway ...Negative regulation of TCF-dependent signaling by DVL-interacting proteins / positive regulation of neuron projection arborization / non-canonical Wnt signaling pathway / WNT5:FZD7-mediated leishmania damping / frizzled binding / PCP/CE pathway / WNT mediated activation of DVL / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Wnt signaling pathway, planar cell polarity pathway / canonical Wnt signaling pathway / positive regulation of GTPase activity / TCF dependent signaling in response to WNT / regulation of actin cytoskeleton organization / positive regulation of JNK cascade / Degradation of DVL / RHO GTPases Activate Formins / beta-catenin binding / small GTPase binding / regulation of protein localization / protease binding / protein stabilization / intracellular signal transduction / response to xenobiotic stimulus / signaling receptor binding / chromatin / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / cytosol
Similarity search - Function
Dishevelled-3 / 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-3 / 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-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsKomarek, J. / Barinka, C.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Czech Academy of Sciences86652036 Czech Republic
CitationJournal: To Be Published
Title: X-ray structure of Dishevelled 3 PDZ domain in complex with C8 peptide
Authors: Komarek, J. / Barinka, C.
History
DepositionFeb 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Segment polarity protein dishevelled homolog DVL-3
A: Segment polarity protein dishevelled homolog DVL-3
P: C8 peptide


Theoretical massNumber of molelcules
Total (without water)24,9513
Polymers24,9513
Non-polymers00
Water1,820101
1
A: Segment polarity protein dishevelled homolog DVL-3
P: C8 peptide

B: Segment polarity protein dishevelled homolog DVL-3


Theoretical massNumber of molelcules
Total (without water)24,9513
Polymers24,9513
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area2400 Å2
ΔGint-16 kcal/mol
Surface area10880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.910, 42.560, 48.290
Angle α, β, γ (deg.)90.00, 96.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Segment polarity protein dishevelled homolog DVL-3 / Dishevelled-3 / DSH homolog 3


Mass: 11988.726 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DVL3, KIAA0208 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92997
#2: Protein/peptide C8 peptide


Mass: 973.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.92 Å3/Da / Density % sol: 35.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2 M ammonium acetate, 0.1 M sodium acetate, 22.5% PEG 4000, 10% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.3418 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Jun 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3418 Å / Relative weight: 1
ReflectionResolution: 1.36→48.02 Å / Num. obs: 40696 / % possible obs: 99.9 % / Redundancy: 7.4 % / CC1/2: 0.998 / Rpim(I) all: 0.02 / Net I/σ(I): 17.3
Reflection shellResolution: 1.36→1.39 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 0.5 / Num. unique obs: 1995 / CC1/2: 0.221 / Rpim(I) all: 1.421 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.36→48.02 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.946 / SU B: 5.433 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24651 2019 5 %RANDOM
Rwork0.18185 ---
obs0.18522 38661 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.73 Å2
Baniso -1Baniso -2Baniso -3
1-1.47 Å2-0 Å23.16 Å2
2---0.49 Å20 Å2
3----1.62 Å2
Refinement stepCycle: 1 / Resolution: 1.36→48.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1535 0 0 101 1636
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131608
X-RAY DIFFRACTIONr_bond_other_d0.0110.0171536
X-RAY DIFFRACTIONr_angle_refined_deg1.881.6322183
X-RAY DIFFRACTIONr_angle_other_deg1.6181.5773571
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6665213
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.62823.42176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.77615284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.823159
X-RAY DIFFRACTIONr_chiral_restr0.1090.2220
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021827
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02308
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_it3.72.914837
X-RAY DIFFRACTIONr_mcbond_other3.7012.914836
X-RAY DIFFRACTIONr_mcangle_it4.7654.3771049
X-RAY DIFFRACTIONr_mcangle_other4.7624.3781050
X-RAY DIFFRACTIONr_scbond_it5.1383.563771
X-RAY DIFFRACTIONr_scbond_other5.1443.565771
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1815.1211132
X-RAY DIFFRACTIONr_long_range_B_refined6.27735.8721673
X-RAY DIFFRACTIONr_long_range_B_other6.27135.8141666
X-RAY DIFFRACTIONr_rigid_bond_restr6.92933144
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.362→1.397 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 122 -
Rwork0.377 2851 -
obs--99.43 %

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