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- PDB-6lcb: Crystal structure of human Dishevelled1 PDZ domain with its inhib... -

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Basic information

Entry
Database: PDB / ID: 6lcb
TitleCrystal structure of human Dishevelled1 PDZ domain with its inhibitor NPL3009
ComponentsSegment polarity protein dishevelled homolog DVL-1
KeywordsSIGNALING PROTEIN / Wnt signaling pathway / Developmental protein / Protein binding / Dvl / INHIBITOR OF PROTEIN-PROTEIN INTERACTIONS
Function / homology
Function and homology information


positive regulation of protein localization to presynapse / Negative regulation of TCF-dependent signaling by DVL-interacting proteins / convergent extension involved in neural plate elongation / skeletal muscle acetylcholine-gated channel clustering / : / cochlea morphogenesis / protein localization to microtubule / positive regulation of neuron projection arborization / presynapse assembly / non-canonical Wnt signaling pathway ...positive regulation of protein localization to presynapse / Negative regulation of TCF-dependent signaling by DVL-interacting proteins / convergent extension involved in neural plate elongation / skeletal muscle acetylcholine-gated channel clustering / : / cochlea morphogenesis / protein localization to microtubule / positive regulation of neuron projection arborization / presynapse assembly / non-canonical Wnt signaling pathway / collateral sprouting / WNT5:FZD7-mediated leishmania damping / neurotransmitter secretion / dendritic spine morphogenesis / frizzled binding / axon extension / PCP/CE pathway / Wnt signalosome / WNT mediated activation of DVL / Disassembly of the destruction complex and recruitment of AXIN to the membrane / neural tube development / Wnt signaling pathway, planar cell polarity pathway / clathrin-coated vesicle / dendrite morphogenesis / regulation of postsynapse organization / regulation of synaptic vesicle exocytosis / neuromuscular junction development / receptor clustering / heart looping / neuronal dense core vesicle / outflow tract morphogenesis / synaptic vesicle exocytosis / social behavior / positive regulation of excitatory postsynaptic potential / protein localization to nucleus / lateral plasma membrane / canonical Wnt signaling pathway / prepulse inhibition / cytoplasmic microtubule organization / negative regulation of protein phosphorylation / axon guidance / TCF dependent signaling in response to WNT / RHO GTPases Activate Formins / Degradation of DVL / synapse organization / Schaffer collateral - CA1 synapse / positive regulation of neuron projection development / small GTPase binding / beta-catenin binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / regulation of protein localization / presynapse / growth cone / cytoplasmic vesicle / microtubule / dendritic spine / postsynaptic density / protein stabilization / intracellular signal transduction / neuron projection / positive regulation of protein phosphorylation / neuronal cell body / glutamatergic synapse / synapse / regulation of DNA-templated transcription / protein kinase binding / enzyme binding / positive regulation of transcription by RNA polymerase II / identical protein binding / cytosol
Similarity search - Function
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. ...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
Chem-E83 / Segment polarity protein dishevelled homolog DVL-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsYasukochi, S. / Numoto, N. / Tenno, N. / Tenno, T. / Ito, N. / Hiroaki, H.
CitationJournal: To Be Published
Title: Crystal structure of human Dishevelled1 PDZ domain with its inhibitor NPL3009
Authors: Yasukochi, S. / Numoto, N. / Tenno, N. / Tenno, T. / Ito, N. / Hiroaki, H.
History
DepositionNov 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 25, 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: Segment polarity protein dishevelled homolog DVL-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3333
Polymers10,7711
Non-polymers5622
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-19 kcal/mol
Surface area5030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.375, 85.375, 46.167
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

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


Mass: 10771.055 Da / Num. of mol.: 1 / Mutation: C338A,W339T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DVL1 / Plasmid: pGEX-6P3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O14640
#2: Chemical ChemComp-E83 / 2-[[3-[(2E)-2-[1,3-bis(oxidanylidene)-1-phenyl-butan-2-ylidene]hydrazinyl]phenyl]sulfonylamino]benzoic acid


Mass: 465.478 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H19N3O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.95 Å3/Da / Density % sol: 37.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.5 M Ammonium sulfate 0.1 M Sodium citrate tribasic dehydrate 1.0 M Lithium sulfate monohydrate 1.0 M Guanidine hydrochloride

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 17013 / % possible obs: 99.5 % / Redundancy: 13.3 % / Biso Wilson estimate: 21.45 Å2 / CC1/2: 1 / Rsym value: 0.04 / Net I/σ(I): 28.5
Reflection shellResolution: 1.4→1.47 Å / Redundancy: 13.7 % / Mean I/σ(I) obs: 2.64 / Num. unique obs: 2661 / CC1/2: 0.861 / Rsym value: 0.882 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LCA

6lca


Resolution: 1.4→40.6 Å / SU ML: 0.1626 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.2392
RfactorNum. reflection% reflection
Rfree0.2298 850 5 %
Rwork0.2142 --
obs0.215 17013 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 25.97 Å2
Refinement stepCycle: LAST / Resolution: 1.4→40.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms614 0 38 43 695
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063751
X-RAY DIFFRACTIONf_angle_d0.86771038
X-RAY DIFFRACTIONf_chiral_restr0.0651119
X-RAY DIFFRACTIONf_plane_restr0.0043136
X-RAY DIFFRACTIONf_dihedral_angle_d22.9361331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.490.31411370.28142613X-RAY DIFFRACTION98.46
1.49-1.60.29711380.25332630X-RAY DIFFRACTION99.18
1.6-1.760.28441400.21892661X-RAY DIFFRACTION99.61
1.76-2.020.24721430.21462702X-RAY DIFFRACTION99.75
2.02-2.540.20251420.2172709X-RAY DIFFRACTION99.96
2.54-40.60.22071500.20582848X-RAY DIFFRACTION99.97

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