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- PDB-6y9p: Crystal structure of Whirlin PDZ3_C-ter in complex with Harmonin ... -

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Basic information

Entry
Database: PDB / ID: 6y9p
TitleCrystal structure of Whirlin PDZ3_C-ter in complex with Harmonin a1 C-terminal PDZ binding motif peptide
Components
  • Harmonin a1
  • Whirlin
KeywordsSTRUCTURAL PROTEIN / Whirlin / PDZ / Myosin 15a / complex
Function / homology
Function and homology information


axon collateral / paranodal junction maintenance / periciliary membrane compartment / USH2 complex / stereocilia ankle link / inner ear receptor cell differentiation / stereocilia ankle link complex / cerebellar Purkinje cell layer formation / sensory perception of light stimulus / photoreceptor connecting cilium ...axon collateral / paranodal junction maintenance / periciliary membrane compartment / USH2 complex / stereocilia ankle link / inner ear receptor cell differentiation / stereocilia ankle link complex / cerebellar Purkinje cell layer formation / sensory perception of light stimulus / photoreceptor connecting cilium / stereocilium tip / inner ear receptor cell stereocilium organization / detection of mechanical stimulus involved in sensory perception of sound / stereocilium bundle / stereocilium / apical dendrite / retina homeostasis / auditory receptor cell stereocilium organization / photoreceptor inner segment / dendritic shaft / ciliary basal body / actin filament / establishment of localization in cell / sensory perception of sound / establishment of protein localization / cilium / actin filament binding / presynapse / growth cone / postsynapse / neuron projection / protein domain specific binding / neuronal cell body / positive regulation of gene expression / perinuclear region of cytoplasm / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Whirlin / : / Harmonin / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily
Similarity search - Domain/homology
Harmonin a1 / Whirlin
Similarity search - Component
Biological speciesMus musculus (house mouse)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.169 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

Downloads & links

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Assembly

Deposited unit
A: Whirlin
B: Whirlin
C: Harmonin a1
D: Harmonin a1
E: Whirlin
F: Harmonin a1
G: Whirlin
H: Harmonin a1
I: Whirlin
J: Harmonin a1
K: Whirlin
L: Harmonin a1


Theoretical massNumber of molelcules
Total (without water)76,58112
Polymers76,58112
Non-polymers00
Water21612
1
A: Whirlin
C: Harmonin a1


Theoretical massNumber of molelcules
Total (without water)12,7642
Polymers12,7642
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-5 kcal/mol
Surface area6440 Å2
MethodPISA
2
B: Whirlin
D: Harmonin a1


Theoretical massNumber of molelcules
Total (without water)12,7642
Polymers12,7642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-5 kcal/mol
Surface area5930 Å2
MethodPISA
3
E: Whirlin
F: Harmonin a1


Theoretical massNumber of molelcules
Total (without water)12,7642
Polymers12,7642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-6 kcal/mol
Surface area6090 Å2
MethodPISA
4
G: Whirlin
H: Harmonin a1


Theoretical massNumber of molelcules
Total (without water)12,7642
Polymers12,7642
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-5 kcal/mol
Surface area6470 Å2
MethodPISA
5
I: Whirlin
J: Harmonin a1


Theoretical massNumber of molelcules
Total (without water)12,7642
Polymers12,7642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint-2 kcal/mol
Surface area5840 Å2
MethodPISA
6
K: Whirlin
L: Harmonin a1


Theoretical massNumber of molelcules
Total (without water)12,7642
Polymers12,7642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint-5 kcal/mol
Surface area5700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.880, 81.030, 111.120
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Whirlin


Mass: 11359.070 Da / Num. of mol.: 6
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
Harmonin a1


Mass: 1404.496 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: Q6PPF3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.26 Å3/Da / Density % sol: 45.57 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris pH 8.5, 0.2M CaCl, 25% 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: Dec 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 3.169→45.82 Å / Num. obs: 10622 / % possible obs: 86.25 % / Redundancy: 3.3 % / CC1/2: 0.987 / CC star: 0.997 / Net I/σ(I): 6.2
Reflection shellResolution: 3.169→3.282 Å / Num. unique obs: 1085 / CC1/2: 0.373 / CC star: 0.737

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Processing

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

1ufx


Resolution: 3.169→45.82 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.277 --
Rwork0.2456 --
obs-10622 86.25 %
Displacement parametersBiso mean: 103.46 Å2
Refinement stepCycle: LAST / Resolution: 3.169→45.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4533 0 0 12 4545
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01074586
X-RAY DIFFRACTIONf_angle_d1.47176164
X-RAY DIFFRACTIONf_chiral_restr0.102720
X-RAY DIFFRACTIONf_plane_restr0.0059797
X-RAY DIFFRACTIONf_dihedral_angle_d23.16671722

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