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- PDB-2kia: Solution structure of Myosin VI C-terminal cargo-binding domain -

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Basic information

Entry
Database: PDB / ID: 2kia
TitleSolution structure of Myosin VI C-terminal cargo-binding domain
ComponentsMyosin-VI
KeywordsMOTOR PROTEIN / Myosin VI / Cargo-binding domain / Molecular motor / Actin-binding / ATP-binding / Calmodulin-binding / Cell projection / Coated pit / Coiled coil / Cytoplasm / Cytoplasmic vesicle / Deafness / Disease mutation / Endocytosis / Golgi apparatus / Hearing / Membrane / Myosin / Nucleotide-binding / Nucleus / Phosphoprotein / Protein transport / Transport
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 / vesicle membrane / vesicle transport along actin filament / glutamate secretion / myosin complex / clathrin-coated vesicle / inner ear morphogenesis / microfilament motor activity / dendrite development / filamentous actin / microvillus / inner ear development / brush border / DNA damage response, signal transduction by p53 class mediator / endocytic vesicle / protein targeting / clathrin-coated pit / ruffle / synapse assembly / presynaptic modulation of chemical synaptic transmission / locomotory behavior / filopodium / actin filament organization / sensory perception of sound / Schaffer collateral - CA1 synapse / regulation of synaptic plasticity / ruffle membrane / endocytosis / actin filament binding / actin cytoskeleton / protein transport / apical part of cell / cytoplasmic vesicle / chemical synaptic transmission / nuclear membrane / postsynaptic density / calmodulin binding / response to xenobiotic stimulus / axon / neuronal cell body / glutamatergic synapse / synapse / perinuclear region of cytoplasm / Golgi apparatus / protein-containing complex / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / Myosin VI, lever arm / 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 VI, lever arm / 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)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsminimized average, model 10
AuthorsFeng, W. / Yu, C. / Wei, Z. / Miyanoiri, Y. / Zhang, M.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2009
Title: Myosin VI undergoes cargo-mediated dimerization
Authors: Yu, C. / Feng, W. / Wei, Z. / Miyanoiri, Y. / Wen, W. / Zhao, Y. / Zhang, M.
History
DepositionApr 29, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myosin-VI


Theoretical massNumber of molelcules
Total (without water)15,3861
Polymers15,3861
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1minimized average

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Components

#1: Protein Myosin-VI /


Mass: 15385.695 Da / Num. of mol.: 1
Fragment: Cargo-binding domain (CBD), UNP residues 1137-1265
Mutation: L73K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Myo6, Sv / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / References: UniProt: Q64331

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1223D 1H-15N NOESY
1333D HN(CA)CB
1433D CBCA(CO)NH
1533D HNCO
1643D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0mM Myosin VI CBD-1, 100% D2O100% D2O
21.0mM [U-100% 15N] Myosin VI CBD-2, 90% H2O/10% D2O90% H2O/10% D2O
31.0mM [U-100% 13C; U-100% 15N] Myosin VI CBD-3, 90% H2O/10% D2O90% H2O/10% D2O
41.0mM [U-100% 13C; U-100% 15N] Myosin VI CBD-4, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMMyosin VI CBD-11
1.0 mMMyosin VI CBD-2[U-100% 15N]2
1.0 mMMyosin VI CBD-3[U-100% 13C; U-100% 15N]3
1.0 mMMyosin VI CBD-4[U-100% 13C; U-100% 15N]4
Sample conditionsIonic strength: 100 / pH: 6.5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA7502

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
PIPPGarrettdata analysis
CNSBrunger, Adams, Clore, Gros, Nilges, Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges, Readrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: minimized average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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