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- PDB-2rey: Crystal structure of the PDZ domain of human dishevelled 2 (homol... -

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Entry
Database: PDB / ID: 2rey
TitleCrystal structure of the PDZ domain of human dishevelled 2 (homologous to Drosophila dsh)
ComponentsSegment polarity protein dishevelled homolog DVL-2
KeywordsGENE REGULATION / PDZ / bound peptide / peptide binding site / Structural Genomics / Structural Genomics Consortium / SGC / Developmental protein / Phosphorylation / Wnt signaling pathway
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 / Resolution: 1.55 Å
AuthorsPapagrigoriou, E. / Gileadi, C. / Elkins, J. / Cooper, C. / Ugochukwu, E. / Turnbull, A. / Pike, A.C.W. / Gileadi, O. / von Delft, F. / Sundstrom, M. ...Papagrigoriou, E. / Gileadi, C. / Elkins, J. / Cooper, C. / Ugochukwu, E. / Turnbull, A. / Pike, A.C.W. / Gileadi, O. / von Delft, F. / Sundstrom, M. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A.M. / Doyle, D. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of the PDZ domains of human dishevelled 2 (homologous to Drosophila dsh).
Authors: Papagrigoriou, E. / Gileadi, C. / Elkins, J. / Cooper, C. / Ugochukwu, E. / Turnbull, A. / Pike, A.C.W. / Gileadi, O. / von Delft, F. / Sundstrom, M. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A.M. / Doyle, D.
History
DepositionSep 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Aug 30, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Segment polarity protein dishevelled homolog DVL-2


Theoretical massNumber of molelcules
Total (without water)10,8221
Polymers10,8221
Non-polymers00
Water75742
1
A: Segment polarity protein dishevelled homolog DVL-2

A: Segment polarity protein dishevelled homolog DVL-2


Theoretical massNumber of molelcules
Total (without water)21,6452
Polymers21,6452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_764-x+2,-x+y+1,-z-1/31
Buried area2440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.644, 69.644, 57.540
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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


Mass: 10822.395 Da / Num. of mol.: 1 / Fragment: PDZ domain: Residues 261-355
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DVL2 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-Rosetta / References: UniProt: O14641
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 1.86 Å3/Da / Density % sol: 33.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2M Ammonium acetate, 0.1M Bis-tris pH 5.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9537 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 3, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.55→34.82 Å / Num. all: 12446 / Num. obs: 12446 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.9 % / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 15.3
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 5.6 / Rsym value: 0.468 / % possible all: 96.1

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Processing

Software
NameVersionClassification
REFMAC5.3.0040refinement
MAR345CCDdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1L6O

1l6o


Resolution: 1.55→34.82 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.996 / SU ML: 0.07 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23982 599 4.8 %RANDOM
Rwork0.21081 ---
all0.21217 11818 --
obs0.21217 11818 99.85 %-
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: 22.157 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20.32 Å20 Å2
2--0.65 Å20 Å2
3----0.97 Å2
Refinement stepCycle: LAST / Resolution: 1.55→34.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms668 0 0 42 710
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022724
X-RAY DIFFRACTIONr_bond_other_d0.0010.02460
X-RAY DIFFRACTIONr_angle_refined_deg1.5491.976990
X-RAY DIFFRACTIONr_angle_other_deg0.93231146
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1385103
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.74325.51729
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.12615129
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.367153
X-RAY DIFFRACTIONr_chiral_restr0.0930.2121
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02816
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02131
X-RAY DIFFRACTIONr_nbd_refined0.1880.2110
X-RAY DIFFRACTIONr_nbd_other0.1850.2466
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2345
X-RAY DIFFRACTIONr_nbtor_other0.090.2426
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.230
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2460.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2570.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2120.29
X-RAY DIFFRACTIONr_mcbond_it3.6565502
X-RAY DIFFRACTIONr_mcbond_other1.4375196
X-RAY DIFFRACTIONr_mcangle_it4.4517761
X-RAY DIFFRACTIONr_scbond_it6.089269
X-RAY DIFFRACTIONr_scangle_it7.6111221
LS refinement shellResolution: 1.55→1.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 52 -
Rwork0.247 827 -
obs--98.43 %
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)
127.0124-0.1101-9.67983.210.77818.40730.3211-1.1751-0.05130.3207-0.16960.05110.0241-0.0406-0.1515-0.0491-0.1119-0.03450.00610.0346-0.129241.853439.13448.5067
218.9388-4.30814.85144.1854-6.330256.36120.1389-1.83140.54930.18580.2917-0.0416-0.61410.2597-0.4306-0.12540.0260.01020.2373-0.0397-0.102828.510341.68882.9517
311.2876-1.8586-14.23636.0524.076733.1906-0.35920.2433-0.01060.00590.0348-0.38551.06560.58930.3244-0.195-0.0046-0.04150.11480.0662-0.083238.520937.7683-7.4681
418.48843.2965-6.463441.4696-22.474426.56010.08160.5862-1.6568-1.1635-0.5247-1.14371.97410.38660.44310.0938-0.0079-0.06760.01140.00610.070445.232534.8271-6.2774
520.0822-15.2647-4.126718.83529.24815.9739-0.1907-0.4731-0.39190.10810.45321.7313-1.3653-0.8205-0.26260.01930.07030.04640.01790.16850.148637.202245.7865-4.2092
613.92772.0126-1.86784.3199-4.7831.54291.3126-0.61311.15950.5414-0.69560.5172-2.0051-0.5136-0.6170.012-0.07560.1424-0.0058-0.0754-0.018337.843846.2485.4828
77.52891.62591.09046.4777-7.276314.75380.20050.01480.4255-0.00170.1211-0.0015-0.3669-0.2977-0.3216-0.1078-0.0713-0.0244-0.05650.0418-0.081645.021543.2631-1.8789
83.5948-3.16881.40185.5188-2.79862.36060.009-0.3193-0.5165-0.3040.22690.77610.1468-0.1337-0.2359-0.1129-0.0804-0.0878-0.05360.12520.049442.006529.92573.7613
911.05972.91612.18211.4334-2.363613.42780.57380.4495-0.6282-0.8902-0.1641-0.03780.51870.2091-0.40970.09280.0102-0.1105-0.11310.0380.027443.871126.8197-3.8301
1019.2598-8.5934-6.95997.41910.9347.15420.3990.2931-1.0508-0.7099-0.34140.5422-0.1036-0.1217-0.0575-0.0092-0.072-0.1676-0.07290.08340.020235.439827.3004-4.1427
1116.93165.1544-4.14182.0963-5.298731.94410.5146-0.53980.1269-0.079-0.18660.3126-1.50960.1071-0.32810.075-0.1048-0.14830.04240.0970.041729.862531.25251.7017
124.459-0.1887-2.91321.4815-0.45093.6421-0.0795-0.3624-0.2772-0.15930.08910.1630.0884-0.0782-0.0096-0.113-0.0962-0.06180.00790.0693-0.060242.138837.68915.403
134.17542.0102-4.92726.0376-10.910334.7648-0.18640.1417-0.1763-0.38790.14480.08610.55710.01590.04160.032-0.13290.0148-0.1233-0.0131-0.09254.532848.5289-9.1748
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA263 - 2734 - 14
2X-RAY DIFFRACTION2AA275 - 27716 - 18
3X-RAY DIFFRACTION3AA278 - 28619 - 27
4X-RAY DIFFRACTION4AA292 - 29533 - 36
5X-RAY DIFFRACTION5AA296 - 30137 - 42
6X-RAY DIFFRACTION6AA302 - 31043 - 51
7X-RAY DIFFRACTION7AA311 - 31652 - 57
8X-RAY DIFFRACTION8AA317 - 32458 - 65
9X-RAY DIFFRACTION9AA325 - 33066 - 71
10X-RAY DIFFRACTION10AA331 - 33772 - 78
11X-RAY DIFFRACTION11AA338 - 34479 - 85
12X-RAY DIFFRACTION12AA345 - 35486 - 95
13X-RAY DIFFRACTION13AA355 - 35996 - 100

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