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- PDB-3cbx: The Dvl2 PDZ Domain in Complex with the C1 Inhibitory Peptide -

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Basic information

Entry
Database: PDB / ID: 3cbx
TitleThe Dvl2 PDZ Domain in Complex with the C1 Inhibitory Peptide
ComponentsDishevelled-2
KeywordsPROTEIN BINDING / PDZ DOMAIN / PHAGE DERIVED HIGH AFFINITY LIGAND / Developmental protein / Phosphoprotein / Wnt signaling pathway / SIGNALING PROTEIN
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 / lateral plasma membrane / canonical Wnt signaling pathway / 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 / : / Cargo recognition for clathrin-mediated endocytosis / apical part of cell / protein-macromolecule adaptor activity / Clathrin-mediated endocytosis / 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 / 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 / Pdz3 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 / Roll / Winged helix-like DNA-binding domain superfamily / Mainly Beta
Similarity search - Domain/homology
Segment polarity protein dishevelled homolog DVL-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsAppleton, B.A. / Wiesmann, C.
CitationJournal: Nat.Chem.Biol. / Year: 2009
Title: Inhibition of Wnt signaling by Dishevelled PDZ peptides
Authors: Zhang, Y. / Appleton, B.A. / Wiesmann, C. / Lau, T. / Costa, M. / Hannoush, R.N. / Sidhu, S.S.
History
DepositionFeb 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dishevelled-2
B: Dishevelled-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1225
Polymers22,8502
Non-polymers2723
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-44 kcal/mol
Surface area11300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.214, 61.112, 65.818
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 11425.021 Da / Num. of mol.: 2 / Fragment: PDZ domain (UNP residues 264-354) / Mutation: C341S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DVL2 / Production host: Escherichia coli (E. coli) / References: UniProt: O14641
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE PEPTIDE LIGAND WAS FUSED TO THE C TERMINUS OF THE LINKER

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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: 2.25 Å3/Da / Density % sol: 45.42 %
Crystal growTemperature: 292 K / pH: 4.8
Details: 60% 2-Methyl-2,4-pentanediol, 0.1 M sodium acetate, pH 4.8, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 23342 / % possible obs: 99.6 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 16.9
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 3.2 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L6O

1l6o


Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.417 / SU ML: 0.076 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1158 5 %RANDOM
Rwork0.185 ---
obs0.187 22027 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.92 Å2
Baniso -1Baniso -2Baniso -3
1--1.83 Å20 Å20 Å2
2--1.54 Å20 Å2
3---0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1558 0 17 121 1696
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221636
X-RAY DIFFRACTIONr_bond_other_d0.0010.021098
X-RAY DIFFRACTIONr_angle_refined_deg1.5361.952217
X-RAY DIFFRACTIONr_angle_other_deg0.89932678
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9225211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.18524.28670
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.49615279
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.276159
X-RAY DIFFRACTIONr_chiral_restr0.0990.2239
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021831
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02328
X-RAY DIFFRACTIONr_nbd_refined0.1970.2247
X-RAY DIFFRACTIONr_nbd_other0.1880.21081
X-RAY DIFFRACTIONr_nbtor_refined0.1810.2757
X-RAY DIFFRACTIONr_nbtor_other0.0830.2891
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.293
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.240.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.5832.51316
X-RAY DIFFRACTIONr_mcbond_other0.7952.5435
X-RAY DIFFRACTIONr_mcangle_it4.151621
X-RAY DIFFRACTIONr_scbond_it3.7632.5741
X-RAY DIFFRACTIONr_scangle_it4.8575591
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.298 48 -
Rwork0.209 1233 -
obs--96.68 %
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)
12.1373-0.39560.65330.9333-0.05260.7083-0.00390.0023-0.1250.01610.04640.02280.0562-0.0377-0.0424-0.0743-0.0082-0.0026-0.08940.0271-0.1037-6.420911.5883-0.8107
24.219-1.58392.17023.8043-1.2594.3537-0.01380.16820.13680.3328-0.1173-0.1033-0.07610.20320.1311-0.0071-0.013-0.0061-0.06760.0132-0.07466.00787.866523.765
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A260 - 355
2X-RAY DIFFRACTION1B356 - 364
3X-RAY DIFFRACTION2B261 - 355
4X-RAY DIFFRACTION2A356 - 364

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