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- PDB-8ard: Myosin VI proximal tail domain, dimeric -

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Basic information

Entry
Database: PDB / ID: 8ard
TitleMyosin VI proximal tail domain, dimeric
ComponentsUnconventional myosin-VI
KeywordsMOTOR PROTEIN / dimer / myosin VI / myo6
Function / homology
Function and homology information


RHOBTB1 GTPase cycle / presynaptic endocytic zone / RHOU GTPase cycle / RHOBTB2 GTPase cycle / Gap junction degradation / cochlear hair cell ribbon synapse / regulation of secretion / Trafficking of AMPA receptors / cellular response to electrical stimulus / postsynaptic neurotransmitter receptor internalization ...RHOBTB1 GTPase cycle / presynaptic endocytic zone / RHOU GTPase cycle / RHOBTB2 GTPase cycle / Gap junction degradation / cochlear hair cell ribbon synapse / regulation of secretion / Trafficking of AMPA receptors / cellular response to electrical stimulus / postsynaptic neurotransmitter receptor internalization / inner ear auditory receptor cell differentiation / postsynaptic actin cytoskeleton / clathrin-coated endocytic vesicle / vesicle membrane / glutamate secretion / vesicle transport along actin filament / myosin complex / inner ear morphogenesis / dendrite development / filamentous actin / inner ear development / microvillus / brush border / cytoskeletal motor activity / endocytic vesicle / DNA damage response, signal transduction by p53 class mediator / protein targeting / clathrin-coated pit / ruffle / synapse assembly / presynaptic modulation of chemical synaptic transmission / locomotory behavior / filopodium / actin filament organization / sensory perception of sound / regulation of synaptic plasticity / Schaffer collateral - CA1 synapse / ruffle membrane / endocytosis / actin filament binding / actin cytoskeleton / apical part of cell / chemical synaptic transmission / cytoplasmic vesicle / nuclear membrane / postsynaptic density / calmodulin binding / response to xenobiotic stimulus / axon / intracellular membrane-bounded organelle / neuronal cell body / glutamatergic synapse / synapse / perinuclear region of cytoplasm / Golgi apparatus / protein-containing complex / nucleoplasm / ATP binding / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Myosin VI, cargo binding domain / Class VI myosin, motor domain / Myosin VI cargo binding domain / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. ...Myosin VI, cargo binding domain / Class VI myosin, motor domain / Myosin VI cargo binding domain / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Unconventional myosin-VI
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.219 Å
AuthorsKikuti, C.M. / Sirkia, H. / Houdusse, A.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-17-CE11-0029-01 France
CitationJournal: Nat Commun / Year: 2023
Title: How myosin VI traps its off-state, is activated and dimerizes.
Authors: Canon, L. / Kikuti, C. / Planelles-Herrero, V.J. / Lin, T. / Mayeux, F. / Sirkia, H. / Lee, Y.I. / Heidsieck, L. / Velikovsky, L. / David, A. / Liu, X. / Moussaoui, D. / Forest, E. / Hook, P. ...Authors: Canon, L. / Kikuti, C. / Planelles-Herrero, V.J. / Lin, T. / Mayeux, F. / Sirkia, H. / Lee, Y.I. / Heidsieck, L. / Velikovsky, L. / David, A. / Liu, X. / Moussaoui, D. / Forest, E. / Hook, P. / Petersen, K.J. / Morgan, T.E. / Di Cicco, A. / Sires-Campos, J. / Derivery, E. / Levy, D. / Delevoye, C. / Sweeney, H.L. / Houdusse, A.
History
DepositionAug 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Unconventional myosin-VI


Theoretical massNumber of molelcules
Total (without water)8,2451
Polymers8,2451
Non-polymers00
Water905
1
A: Unconventional myosin-VI

A: Unconventional myosin-VI


Theoretical massNumber of molelcules
Total (without water)16,4892
Polymers16,4892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Buried area2150 Å2
ΔGint-23 kcal/mol
Surface area10530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.387, 29.387, 295.649
Angle α, β, γ (deg.)90, 90, 120
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Unconventional myosin-VI / / Unconventional myosin-6


Mass: 8244.524 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Myo6 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E9Q3L1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.23 Å3/Da / Density % sol: 45.1 % / Description: thin rods
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 27% PEG 4000, 10 mM MgCl2, 0.2 M imidazole-malate, pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.219→49.27 Å / Num. obs: 2977 / % possible obs: 66.9 % / Observed criterion σ(I): 1.2 / Redundancy: 18.2 % / Biso Wilson estimate: 39.2 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.168 / Rrim(I) all: 0.174 / Net I/σ(I): 11.7
Reflection shellResolution: 2.219→2.458 Å / Redundancy: 14 % / Rmerge(I) obs: 2.414 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 199 / CC1/2: 0.598 / Rrim(I) all: 2.506 / % possible all: 55.9

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (8-JUN-2022)refinement
XDS20180409data reduction
STARANISO1.10.15data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 30x Ser helix

Resolution: 2.219→49.27 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.912 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.899 / SU Rfree Blow DPI: 0.384
RfactorNum. reflection% reflectionSelection details
Rfree0.3381 301 -RANDOM
Rwork0.3227 ---
obs0.3243 2977 66.9 %-
Displacement parametersBiso mean: 55.93 Å2
Baniso -1Baniso -2Baniso -3
1-3.6589 Å20 Å20 Å2
2--3.6589 Å20 Å2
3----7.3178 Å2
Refine analyzeLuzzati coordinate error obs: 0.63 Å
Refinement stepCycle: LAST / Resolution: 2.219→49.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms512 0 0 5 517
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081046HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.971904HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d348SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes159HARMONIC5
X-RAY DIFFRACTIONt_it512HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion69SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact891SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.6
X-RAY DIFFRACTIONt_other_torsion20.58
LS refinement shellResolution: 2.22→2.46 Å
RfactorNum. reflection% reflection
Rfree0.3562 23 -
Rwork0.3662 --
obs0.3649 199 17.57 %
Refinement TLS params.Origin x: -8.4193 Å / Origin y: 12.577 Å / Origin z: 8.0757 Å
111213212223313233
T0.3322 Å20.0625 Å2-0.1003 Å2--0.1552 Å20.0064 Å2---0.1929 Å2
L1.4077 °20.2596 °21.0147 °2-0.4637 °2-5.23 °2--16.6309 °2
S-0.2217 Å °0.1845 Å °-0.9746 Å °0.1845 Å °-0.3542 Å °-0.2437 Å °-0.9746 Å °-0.2437 Å °0.576 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A876 - 937
2X-RAY DIFFRACTION1{ A|* }A1001 - 1005

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