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- PDB-6y38: Crystal structure of Whirlin PDZ3 in complex with Myosin 15a C-te... -

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Basic information

Entry
Database: PDB / ID: 6y38
TitleCrystal structure of Whirlin PDZ3 in complex with Myosin 15a C-terminal PDZ binding motif peptide
Components
  • Chains: C,D
  • Whirlin
KeywordsSTRUCTURAL PROTEIN / Whirlin / PDZ / Myosin 15a / complex
Function / homology
Function and homology information


axon collateral / paranodal junction maintenance / periciliary membrane compartment / stereocilia ankle link / actin-based cell projection / USH2 complex / inner ear receptor cell differentiation / stereocilia ankle link complex / sensory perception of light stimulus / cerebellar Purkinje cell layer formation ...axon collateral / paranodal junction maintenance / periciliary membrane compartment / stereocilia ankle link / actin-based cell projection / USH2 complex / inner ear receptor cell differentiation / stereocilia ankle link complex / sensory perception of light stimulus / cerebellar Purkinje cell layer formation / photoreceptor connecting cilium / inner ear receptor cell stereocilium organization / stereocilium tip / stereocilium bundle / detection of mechanical stimulus involved in sensory perception of sound / stereocilium / apical dendrite / retina homeostasis / auditory receptor cell stereocilium organization / myosin complex / inner ear morphogenesis / microfilament motor activity / response to light stimulus / photoreceptor inner segment / ciliary basal body / dendritic shaft / actin filament organization / establishment of localization in cell / actin filament / locomotory behavior / sensory perception of sound / establishment of protein localization / cilium / endocytosis / actin filament binding / actin cytoskeleton / presynapse / growth cone / postsynapse / neuron projection / protein domain specific binding / neuronal cell body / positive regulation of gene expression / perinuclear region of cytoplasm / ATP binding / identical protein binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Whirlin / : / Class XV myosin, motor domain / Myosin-XV, FERM domain C-lobe / : / : / MyTH4 domain / MyTH4 domain superfamily / MyTH4 domain / MyTH4 domain profile. ...Whirlin / : / Class XV myosin, motor domain / Myosin-XV, FERM domain C-lobe / : / : / MyTH4 domain / MyTH4 domain superfamily / MyTH4 domain / MyTH4 domain profile. / Domain in Myosin and Kinesin Tails / IQ calmodulin-binding motif / Variant SH3 domain / FERM central domain / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Kinesin motor domain superfamily / 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 / PH-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Whirlin / Unconventional myosin-XV
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.697 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
DepositionFeb 17, 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
B: Whirlin
C: Chains: C,D
D: Chains: C,D


Theoretical massNumber of molelcules
Total (without water)24,9974
Polymers24,9974
Non-polymers00
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-20 kcal/mol
Surface area10510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.140, 112.920, 34.630
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Whirlin


Mass: 11015.586 Da / Num. of mol.: 2
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 Chains: C,D


Mass: 1482.741 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9QZZ4*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.12 Å3/Da / Density % sol: 41.91 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.1M trisodium citrate pH 5.6, 20% v/v isopropanol, 20% w/v PEG 4000,

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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: May 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.697→34.63 Å / Num. obs: 22938 / % possible obs: 94.46 % / Redundancy: 7 % / CC1/2: 0.998 / CC star: 0.999 / Net I/σ(I): 15.14
Reflection shellResolution: 1.697→1.758 Å / Num. unique obs: 1615 / CC1/2: 0.735

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Processing

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

1ufx


Resolution: 1.697→34.63 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2307 --
Rwork0.2072 --
obs-22938 94.46 %
Displacement parametersBiso mean: 26.77 Å2
Refinement stepCycle: LAST / Resolution: 1.697→34.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1615 0 0 218 1833
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01131634
X-RAY DIFFRACTIONf_angle_d1.38572203
X-RAY DIFFRACTIONf_chiral_restr0.1087265
X-RAY DIFFRACTIONf_plane_restr0.0087283
X-RAY DIFFRACTIONf_dihedral_angle_d22.2082624

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