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- PDB-6kz1: Complex structure of Whirlin and Myosin XVa -

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Basic information

Entry
Database: PDB / ID: 6kz1
TitleComplex structure of Whirlin and Myosin XVa
Components
  • Myosin XVa
  • Whirlin
KeywordsMOTOR PROTEIN / Whirlin / Myosin XVa / complex structure
Function / homology
Function and homology information


paranodal junction maintenance / microfilament motor activity => GO:0000146 / periciliary membrane compartment / USH2 complex / stereocilia ankle link / actin-based cell projection / inner ear receptor cell differentiation / stereocilia ankle link complex / sensory perception of light stimulus / cerebellar Purkinje cell layer formation ...paranodal junction maintenance / microfilament motor activity => GO:0000146 / periciliary membrane compartment / USH2 complex / stereocilia ankle link / actin-based cell projection / inner ear receptor cell differentiation / stereocilia ankle link complex / sensory perception of light stimulus / cerebellar Purkinje cell layer formation / photoreceptor connecting cilium / stereocilium tip / inner ear receptor cell stereocilium organization / detection of mechanical stimulus involved in sensory perception of sound / stereocilium / vesicle transport along actin filament / retina homeostasis / auditory receptor cell stereocilium organization / myosin complex / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / microfilament motor activity / photoreceptor inner segment / ciliary basal body / establishment of localization in cell / actin filament / actin filament organization / sensory perception of sound / establishment of protein localization / cilium / actin filament binding / actin cytoskeleton / growth cone / vesicle / calmodulin binding / synapse / positive regulation of gene expression / extracellular exosome / ATP binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Unconventional myosin-XV / 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 ...Unconventional myosin-XV / 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 / Short calmodulin-binding motif containing conserved Ile and Gln residues. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / IQ motif, EF-hand binding site / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.694 Å
AuthorsLin, L. / Wang, M. / Shi, Y. / Zhu, J. / Zhang, R.
CitationJournal: Cell Rep / Year: 2021
Title: Phase separation-mediated condensation of Whirlin-Myo15-Eps8 stereocilia tip complex.
Authors: Lin, L. / Shi, Y. / Wang, M. / Wang, C. / Lu, Q. / Zhu, J. / Zhang, R.
History
DepositionSep 22, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 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
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: Myosin XVa


Theoretical massNumber of molelcules
Total (without water)14,0422
Polymers14,0422
Non-polymers00
Water95553
1
A: Whirlin

B: Myosin XVa


Theoretical massNumber of molelcules
Total (without water)14,0422
Polymers14,0422
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z+1/31
Buried area1160 Å2
ΔGint-11 kcal/mol
Surface area6130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.974, 51.974, 70.445
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-1023-

HOH

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Components

#1: Protein Whirlin / Autosomal recessive deafness type 31 protein


Mass: 12430.313 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WHRN, DFNB31, KIAA1526 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9P202
#2: Protein/peptide Myosin XVa


Mass: 1611.920 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UKN7*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 1.96 Å3/Da / Density % sol: 37.12 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: Potassium phosphate dibasic, HEPES pH7.5, Sodium phosphate monobasi

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.69→45.011 Å / Num. obs: 23647 / % possible obs: 99.8 % / Redundancy: 10.261 % / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rrim(I) all: 0.057 / Χ2: 1.13 / Net I/σ(I): 22.54 / Num. measured all: 242635
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.69-1.89.8130.6853.1237386385938100.9280.72298.7
1.8-1.9210.3190.396.2236695355735560.9820.411100
1.92-2.0710.860.20112.2936632337333730.9950.211100
2.07-2.2710.6180.12119.8632692307930790.9970.127100
2.27-2.549.6650.08425.5826819277527750.9980.089100
2.54-2.939.9660.06234.0624765248524850.9990.066100
2.93-3.5810.660.04748.6621927205720570.9990.049100
3.58-5.0510.1040.03855.1116368162016200.9990.04100
5.05-45.01110.4830.03557.7193518928920.9990.037100

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UFX

1ufx


Resolution: 1.694→45.011 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 21.6
RfactorNum. reflection% reflection
Rfree0.2008 637 5.03 %
Rwork0.1787 --
obs0.1798 12670 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.41 Å2 / Biso mean: 34.83 Å2 / Biso min: 17.83 Å2
Refinement stepCycle: final / Resolution: 1.694→45.011 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms811 0 0 53 864
Biso mean---42.96 -
Num. residues----109
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012819
X-RAY DIFFRACTIONf_angle_d1.4241108
X-RAY DIFFRACTIONf_chiral_restr0.06137
X-RAY DIFFRACTIONf_plane_restr0.007141
X-RAY DIFFRACTIONf_dihedral_angle_d13.155301
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.694-1.82470.2411260.2211233399
1.8247-2.00830.23131280.18722371100
2.0083-2.29890.18731290.17272379100
2.2989-2.89640.24121230.20852423100
2.8964-45.0110.18251310.16452527100
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)
10.16490.34060.25240.70610.66490.61750.0002-0.4190.04210.1469-0.09070.15140.0667-0.2076-0.08820.2229-0.0805-0.0310.31020.01430.228-11.032717.75465.8321
21.25020.66320.73180.65410.26880.4729-0.83070.19410.9039-0.820.20230.5284-0.6746-0.1388-0.01110.2807-0.0834-0.08680.25880.00920.2452-10.216625.4206-6.9816
30.03810.02810.0360.03940.01640.01520.1848-0.4660.5580.38910.0653-0.08140.1040.4163-0.00030.2459-0.0266-0.00860.3238-0.05120.27315.694327.21161.9601
40.0778-0.0498-0.08990.08030.05230.1125-0.26960.39980.3992-0.36090.29420.1342-0.21660.3255-0.00090.2828-0.0514-0.04580.18240.02670.2738-6.958931.589-0.2822
50.34840.5138-0.03170.5660.12170.26290.0951-0.0369-0.0638-0.0408-0.15060.3093-0.0143-0.0957-0.00020.2423-0.0064-0.05690.2354-0.03240.2833-11.667925.40970.3936
60.0813-0.0683-0.06710.11530.11360.1030.06240.2648-0.88020.036-0.0135-0.37440.27730.4995-0.00280.23480.0002-0.06310.31160.00630.33992.790717.5046-0.0431
70.0095-0.00610.01180.12420.13530.0624-0.63840.8327-0.3513-0.66220.5429-0.0475-0.11770.31080.00070.3012-0.0780.04620.3479-0.06640.2528-1.383719.92-8.8304
80.8049-0.2626-0.40580.2550.21690.4541-0.1923-0.254-0.67610.47790.0185-0.02150.55840.1024-0.0010.3162-0.03260.0370.2195-0.02850.4497-12.299410.6831-9.6896
90.1186-0.013-0.02790.0473-0.06410.07050.0088-0.0696-0.29830.20970.0369-0.20260.0677-0.07880.00110.2583-0.0483-0.0290.24040.00840.2399-9.031217.64791.6248
100.0240.0730.03530.07450.01770.05350.3902-0.0671-0.38980.4837-0.1029-0.19240.029-0.3226-0.00240.3667-0.037-0.01420.4003-0.04090.25720.334827.885911.2051
110.04540.1098-0.01240.0254-0.01050.1221-0.1268-0.51770.004-0.3547-0.169-0.13870.14910.21480.00110.2741-0.0526-0.00940.34960.04390.30123.912234.3247-11.9894
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 811 through 820 )A811 - 820
2X-RAY DIFFRACTION2chain 'A' and (resid 821 through 831 )A821 - 831
3X-RAY DIFFRACTION3chain 'A' and (resid 832 through 841 )A832 - 841
4X-RAY DIFFRACTION4chain 'A' and (resid 842 through 846 )A842 - 846
5X-RAY DIFFRACTION5chain 'A' and (resid 847 through 867 )A847 - 867
6X-RAY DIFFRACTION6chain 'A' and (resid 868 through 876 )A868 - 876
7X-RAY DIFFRACTION7chain 'A' and (resid 877 through 889 )A877 - 889
8X-RAY DIFFRACTION8chain 'A' and (resid 890 through 894 )A890 - 894
9X-RAY DIFFRACTION9chain 'A' and (resid 895 through 901 )A895 - 901
10X-RAY DIFFRACTION10chain 'A' and (resid 902 through 907 )A902 - 907
11X-RAY DIFFRACTION11chain 'B' and (resid 3500 through 3511 )B0

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