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- PDB-6fdd: Crystal Structure of the HHD2 Domain of Whirlin -

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Basic information

Entry
Database: PDB / ID: 6fdd
TitleCrystal Structure of the HHD2 Domain of Whirlin
ComponentsWhirlin
KeywordsSTRUCTURAL PROTEIN / Usher syndrome / scaffold protein / hearing / deafness
Function / homology
Function and homology information


paranodal junction maintenance / stereocilia ankle link / USH2 complex / periciliary membrane compartment / stereocilia ankle link complex / inner ear receptor cell differentiation / sensory perception of light stimulus / cerebellar Purkinje cell layer formation / stereocilium tip / photoreceptor connecting cilium ...paranodal junction maintenance / stereocilia ankle link / USH2 complex / periciliary membrane compartment / stereocilia ankle link complex / inner ear receptor cell differentiation / sensory perception of light stimulus / cerebellar Purkinje cell layer formation / stereocilium tip / photoreceptor connecting cilium / inner ear receptor cell stereocilium organization / stereocilium bundle / detection of mechanical stimulus involved in sensory perception of sound / stereocilium / retina homeostasis / auditory receptor cell stereocilium organization / photoreceptor inner segment / actin filament / establishment of protein localization / establishment of localization in cell / sensory perception of sound / growth cone / neuron projection / cilium / ciliary basal body / synapse / positive regulation of gene expression / identical protein binding / cytosol
Similarity search - Function
Whirlin / : / : / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsDelhommel, F. / Cordier, F. / Saul, F. / Haouz, A. / Wolff, N.
Funding support France, 3items
OrganizationGrant numberCountry
Fondation de France-Committee Berthe Fouassier France
Institut Pasteur France
Ministere de l'Enseignement Superieur et de la Recherche France
CitationJournal: FEBS J. / Year: 2018
Title: Structural plasticity of the HHD2 domain of whirlin.
Authors: Delhommel, F. / Cordier, F. / Saul, F. / Chataigner, L. / Haouz, A. / Wolff, N.
History
DepositionDec 22, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Whirlin
D: Whirlin
E: Whirlin
F: Whirlin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,17213
Polymers59,4996
Non-polymers6727
Water10,845602
1
A: Whirlin


Theoretical massNumber of molelcules
Total (without water)9,9171
Polymers9,9171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Whirlin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1093
Polymers9,9171
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Whirlin


Theoretical massNumber of molelcules
Total (without water)9,9171
Polymers9,9171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Whirlin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0132
Polymers9,9171
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Whirlin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0132
Polymers9,9171
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Whirlin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2054
Polymers9,9171
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.580, 74.910, 63.840
Angle α, β, γ (deg.)90.00, 106.38, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Whirlin


Mass: 9916.566 Da / Num. of mol.: 6 / Fragment: WHIRLIN DOMAIN HHD2 RESIDUES 420-499
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Whrn, Dfnb31, Kiaa1526 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q80VW5
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 602 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.34 Å3/Da / Density % sol: 47.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: ammonium sulfate 1.26M cacodylate 0.7M

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97917 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
ReflectionResolution: 1.75→49.17 Å / Num. obs: 54049 / % possible obs: 99.9 % / Redundancy: 5.5 % / Biso Wilson estimate: 27.66 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.047 / Net I/σ(I): 13
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2966 / CC1/2: 0.681 / Rpim(I) all: 0.63 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PARROTphasing
ARP/wARPmodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.75→47.61 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / SU R Cruickshank DPI: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.121 / SU Rfree Blow DPI: 0.108 / SU Rfree Cruickshank DPI: 0.104
RfactorNum. reflection% reflectionSelection details
Rfree0.21 2697 5 %RANDOM
Rwork0.187 ---
obs0.188 53949 99.8 %-
Displacement parametersBiso mean: 30.55 Å2
Baniso -1Baniso -2Baniso -3
1--3.0504 Å20 Å2-0.8912 Å2
2--1.9108 Å20 Å2
3---1.1396 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: 1 / Resolution: 1.75→47.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3647 0 35 602 4284
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013791HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.835131HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1381SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes89HARMONIC2
X-RAY DIFFRACTIONt_gen_planes564HARMONIC5
X-RAY DIFFRACTIONt_it3791HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.67
X-RAY DIFFRACTIONt_other_torsion16.24
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion496SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5000SEMIHARMONIC4
LS refinement shellResolution: 1.75→1.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3697 198 5.02 %
Rwork0.3195 3750 -
all0.3219 3948 -
obs--99.82 %

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