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- PDB-6y9o: Crystal structure of Whirlin PDZ3_C-ter in complex with CASK inte... -

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Basic information

Entry
Database: PDB / ID: 6y9o
TitleCrystal structure of Whirlin PDZ3_C-ter in complex with CASK internal PDZ binding motif peptide
Components
  • Peripheral plasma membrane protein CASK
  • Whirlin
KeywordsSTRUCTURAL PROTEIN / Whirlin / PDZ / Myosin 15a / complex
Function / homology
Function and homology information


Dopamine Neurotransmitter Release Cycle / paranodal junction maintenance / stereocilia ankle link / USH2 complex / periciliary membrane compartment / Neurexins and neuroligins / stereocilia ankle link complex / negative regulation of cellular response to growth factor stimulus / inner ear receptor cell differentiation / sensory perception of light stimulus ...Dopamine Neurotransmitter Release Cycle / paranodal junction maintenance / stereocilia ankle link / USH2 complex / periciliary membrane compartment / Neurexins and neuroligins / stereocilia ankle link complex / negative regulation of cellular response to growth factor stimulus / inner ear receptor cell differentiation / sensory perception of light stimulus / cerebellar Purkinje cell layer formation / stereocilium tip / neurexin family protein binding / photoreceptor connecting cilium / inner ear receptor cell stereocilium organization / negative regulation of wound healing / stereocilium bundle / detection of mechanical stimulus involved in sensory perception of sound / nuclear lamina / stereocilium / retina homeostasis / calcium ion import / auditory receptor cell stereocilium organization / positive regulation of calcium ion import / regulation of synaptic vesicle exocytosis / basement membrane / negative regulation of cell-matrix adhesion / negative regulation of keratinocyte proliferation / photoreceptor inner segment / actin filament / establishment of localization in cell / establishment of protein localization / sensory perception of sound / Schaffer collateral - CA1 synapse / nuclear matrix / cell-cell junction / growth cone / basolateral plasma membrane / vesicle / calmodulin binding / non-specific serine/threonine protein kinase / neuron projection / cilium / ciliary basal body / protein serine kinase activity / protein serine/threonine kinase activity / synapse / positive regulation of gene expression / nucleolus / positive regulation of transcription by RNA polymerase II / ATP binding / identical protein binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
Whirlin / : / CASK, SH3 domain / : / L27 domain, C-terminal / L27 domain / : / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. ...Whirlin / : / CASK, SH3 domain / : / L27 domain, C-terminal / L27 domain / : / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Variant SH3 domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / PDZ 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 / Protein kinase domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Peripheral plasma membrane protein CASK / Whirlin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.632 Å
AuthorsZhu, Y. / Delhommel, F. / Haouz, A. / Caillet-Saguy, C. / Vaney, M. / Mechaly, A.E. / Wolff, N.
Funding support France, 1items
OrganizationGrant numberCountry
Marie Sklodowska-Curie Actions, FragNET ITN675341 France
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Deciphering the Unexpected Binding Capacity of the Third PDZ Domain of Whirlin to Various Cochlear Hair Cell Partners.
Authors: Zhu, Y. / Delhommel, F. / Cordier, F. / Luchow, S. / Mechaly, A. / Colcombet-Cazenave, B. / Girault, V. / Pepermans, E. / Bahloul, A. / Gautier, C. / Brule, S. / Raynal, B. / Hoos, S. / ...Authors: Zhu, Y. / Delhommel, F. / Cordier, F. / Luchow, S. / Mechaly, A. / Colcombet-Cazenave, B. / Girault, V. / Pepermans, E. / Bahloul, A. / Gautier, C. / Brule, S. / Raynal, B. / Hoos, S. / Haouz, A. / Caillet-Saguy, C. / Ivarsson, Y. / Wolff, N.
History
DepositionMar 10, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Jan 24, 2024Group: 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: Whirlin
C: Peripheral plasma membrane protein CASK


Theoretical massNumber of molelcules
Total (without water)12,7922
Polymers12,7922
Non-polymers00
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-9 kcal/mol
Surface area5800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.470, 50.470, 88.410
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-1008-

HOH

21A-1055-

HOH

31A-1101-

HOH

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Components

#1: Protein Whirlin


Mass: 11359.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Whrn, Dfnb31, Kiaa1526
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q80VW5
#2: Protein/peptide Peripheral plasma membrane protein CASK / Calcium/calmodulin-dependent serine protein kinase


Mass: 1432.619 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
References: UniProt: O70589, non-specific serine/threonine protein kinase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.54 Å3/Da / Density % sol: 51.6 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M LiCl, 25 %w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Nov 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.632→39.18 Å / Num. obs: 16757 / % possible obs: 99.73 % / Redundancy: 19.2 % / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 26.04
Reflection shellResolution: 1.632→1.691 Å / Num. unique obs: 1614 / CC1/2: 0.945 / CC star: 0.986

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Processing

Software
NameClassification
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UFX

1ufx


Resolution: 1.632→39.18 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2286 --
Rwork0.2073 --
obs-16757 99.73 %
Displacement parametersBiso mean: 21.11 Å2
Refinement stepCycle: LAST / Resolution: 1.632→39.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms809 0 0 113 922
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057830
X-RAY DIFFRACTIONf_angle_d0.83021123
X-RAY DIFFRACTIONf_chiral_restr0.0589131
X-RAY DIFFRACTIONf_plane_restr0.0045145
X-RAY DIFFRACTIONf_dihedral_angle_d18.0672314

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