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- PDB-2ld3: Solution structure of myosin VI lever arm extension -

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Basic information

Entry
Database: PDB / ID: 2ld3
TitleSolution structure of myosin VI lever arm extension
ComponentsMyosin VI
KeywordsMOTOR PROTEIN / molecular motor / myosin VI / lever arm extension
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 / cytoskeletal motor activity / 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 / synapse / glutamatergic 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-6 / Unconventional myosin-VI
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsminimized average structure, model 10
Model type detailsminimized average
AuthorsFeng, W. / Yu, C. / Zhang, M.
CitationJournal: To be Published
Title: Membrane-induced lever arm expansion allows myosin VI to walk with large and variable step sizes
Authors: Yu, C. / Feng, W. / Lou, J. / Wu, J. / Pan, L. / Zhang, M.
History
DepositionMay 13, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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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)9,9621
Polymers9,9621
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein Myosin VI /


Mass: 9961.551 Da / Num. of mol.: 1 / Fragment: residues in UNP 840-922
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Myo6 / Production host: Escherichia coli (E. coli) / References: UniProt: B2RWR8, UniProt: Q64331*PLUS

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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
11.0 mM myosin VI LAE-1, 100% D2O100% D2O
21.0 mM [U-100% 15N] myosin VI LAE-2, 90% H2O/10% D2O90% H2O/10% D2O
31.0 mM [U-100% 13C; U-100% 15N] myosin VI LAE-3, 90% H2O/10% D2O90% H2O/10% D2O
41.0 mM [U-100% 13C; U-100% 15N] myosin VI LAE-4, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMmyosin VI LAE-11
1.0 mMmyosin VI LAE-2[U-100% 15N]2
1.0 mMmyosin VI LAE-3[U-100% 13C; U-100% 15N]3
1.0 mMmyosin VI LAE-4[U-100% 13C; U-100% 15N]4
Sample conditionsIonic strength: 50 / 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 and Readstructure solution
CNSrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 10

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