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- PDB-8yr7: Crystal structure of human dishevelled 2 (Dvl2) PDZ domain fused ... -

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Basic information

Entry
Database: PDB / ID: 8yr7
TitleCrystal structure of human dishevelled 2 (Dvl2) PDZ domain fused with WGEF internal peptide motif
ComponentsSegment polarity protein dishevelled homolog DVL-2,Rho guanine nucleotide exchange factor 19
KeywordsSIGNALING PROTEIN / Wnt signaling
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 / 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 / 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 / clathrin-coated endocytic vesicle / WNT5:FZD7-mediated leishmania damping / 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 / regulation of small GTPase mediated signal transduction / Wnt signaling pathway, planar cell polarity pathway / NRAGE signals death through JNK / heart looping / outflow tract morphogenesis / CDC42 GTPase cycle / lateral plasma membrane / RHOA GTPase cycle / canonical Wnt signaling pathway / positive regulation of JUN kinase activity / RAC1 GTPase cycle / GTPase activator activity / guanyl-nucleotide exchange factor activity / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / neural tube closure / Degradation of DVL / RHO GTPases Activate Formins / regulation of actin cytoskeleton organization / positive regulation of JNK cascade / wound healing / protein localization / small GTPase binding / positive regulation of DNA-binding transcription factor activity / : / G alpha (12/13) signalling events / Cargo recognition for clathrin-mediated endocytosis / apical part of cell / Clathrin-mediated endocytosis / protein-macromolecule adaptor activity / 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 / cytoplasm / cytosol
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 ...: / : / 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 / Variant SH3 domain / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / PH domain profile. / PDZ domain / Pleckstrin homology domain. / Pleckstrin homology domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain 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 / Rho guanine nucleotide exchange factor 19
Similarity search - Component
Biological speciessynthetic construct (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsOmble, A. / Mahajan, S. / Kulkarni, K.A.
Funding support India, 1items
OrganizationGrant numberCountry
Council of Scientific & Industrial Research (CSIR) India
CitationJournal: Commun Biol / Year: 2024
Title: Dishevelled2 activates WGEF via its interaction with a unique internal peptide motif of the GEF.
Authors: Omble, A. / Mahajan, S. / Bhoite, A. / Kulkarni, K.
History
DepositionMar 20, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 2024Provider: repository / Type: Initial release

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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,Rho guanine nucleotide exchange factor 19


Theoretical massNumber of molelcules
Total (without water)11,6071
Polymers11,6071
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.491, 59.491, 58.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Space group name HallI4bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1,x+1/2,z+5/4
#7: y+1,-x+1/2,z+5/4
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Segment polarity protein dishevelled homolog DVL-2,Rho guanine nucleotide exchange factor 19 / Dishevelled-2 / DSH homolog 2 / Ephexin-2


Mass: 11607.190 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others), (gene. exp.) Homo sapiens (human)
Gene: DVL2, ARHGEF19 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: O14641, UniProt: Q8IW93

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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: 2.22 Å3/Da / Density % sol: 44.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 0.1M Sodium acetate (pH 4.5), 3M Sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97893 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Feb 4, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97893 Å / Relative weight: 1
ReflectionResolution: 3→42.07 Å / Num. obs: 2071 / % possible obs: 99.9 % / Redundancy: 14.9 % / Biso Wilson estimate: 90.9 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.058 / Net I/σ(I): 27.8
Reflection shellResolution: 3→3.19 Å / Redundancy: 15.1 % / Rmerge(I) obs: 1.091 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 336 / CC1/2: 0.731 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→29.75 Å / SU ML: 0.1661 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 32.5656
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.335 116 5.61 %
Rwork0.2995 1951 -
obs0.3011 2067 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 114.33 Å2
Refinement stepCycle: LAST / Resolution: 3→29.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms512 0 0 0 512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087512
X-RAY DIFFRACTIONf_angle_d1.361697
X-RAY DIFFRACTIONf_chiral_restr0.089796
X-RAY DIFFRACTIONf_plane_restr0.003588
X-RAY DIFFRACTIONf_dihedral_angle_d10.7099161
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.140.3315150.3633239X-RAY DIFFRACTION100
3.14-3.310.3114140.3601244X-RAY DIFFRACTION100
3.31-3.510.5196280.3126230X-RAY DIFFRACTION100
3.52-3.780.38650.3231249X-RAY DIFFRACTION99.61
3.78-4.160.670170.3226249X-RAY DIFFRACTION100
4.16-4.760.2585180.2691238X-RAY DIFFRACTION100
4.78-5.990.2801260.3288237X-RAY DIFFRACTION100
6-29.750.368230.2754265X-RAY DIFFRACTION99.63
Refinement TLS params.Method: refined / Origin x: 17.2094694019 Å / Origin y: -1.26016011047 Å / Origin z: 2.01486071543 Å
111213212223313233
T0.683891945094 Å20.0250717580262 Å20.279564584964 Å2-1.18355767924 Å20.0511201208865 Å2--0.78280089727 Å2
L12.720025874 °22.63393625311 °23.88137921474 °2-9.53458052267 °2-0.949275487334 °2--13.215663893 °2
S0.79914492047 Å °1.78831674028 Å °1.54615072569 Å °0.564632797859 Å °-0.909977003213 Å °0.802202708398 Å °0.304957622383 Å °-0.266063912403 Å °0.0214749664821 Å °
Refinement TLS groupSelection details: all

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