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- PDB-2n11: Solution structure of human Myosin VI isoform3 (998-1071) -

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Basic information

Entry
Database: PDB / ID: 2n11
TitleSolution structure of human Myosin VI isoform3 (998-1071)
ComponentsUnconventional myosin-VI
KeywordsMOTOR PROTEIN / PROTEIN TRANSPORT
Function / homology
Function and homology information


regulation of secretion / minus-end directed microfilament motor activity / unconventional myosin complex / actin filament-based movement / inner ear auditory receptor cell differentiation / clathrin-coated vesicle membrane / Gap junction degradation / vesicle transport along actin filament / Trafficking of AMPA receptors / RHOBTB1 GTPase cycle ...regulation of secretion / minus-end directed microfilament motor activity / unconventional myosin complex / actin filament-based movement / inner ear auditory receptor cell differentiation / clathrin-coated vesicle membrane / Gap junction degradation / vesicle transport along actin filament / Trafficking of AMPA receptors / RHOBTB1 GTPase cycle / inner ear morphogenesis / microfilament motor activity / cytoskeletal motor activity / filamentous actin / microvillus / RHOU GTPase cycle / DNA damage response, signal transduction by p53 class mediator / endocytic vesicle / autophagosome / RHOBTB2 GTPase cycle / clathrin-coated pit / ruffle / filopodium / actin filament / actin filament organization / sensory perception of sound / intracellular protein transport / protein localization / ADP binding / ruffle membrane / endocytosis / actin filament binding / actin cytoskeleton / apical part of cell / actin binding / cell cortex / cytoplasmic vesicle / nuclear membrane / calmodulin binding / endosome / response to xenobiotic stimulus / lysosomal membrane / perinuclear region of cytoplasm / Golgi apparatus / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol
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 speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsHe, F. / Walters, K.
CitationJournal: Cell Rep / Year: 2016
Title: Myosin VI Contains a Compact Structural Motif that Binds to Ubiquitin Chains.
Authors: He, F. / Wollscheid, H.P. / Nowicka, U. / Biancospino, M. / Valentini, E. / Ehlinger, A. / Acconcia, F. / Magistrati, E. / Polo, S. / Walters, K.J.
History
DepositionMar 20, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 1.2Apr 6, 2016Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Unconventional myosin-VI


Theoretical massNumber of molelcules
Total (without water)8,3991
Polymers8,3991
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

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


Mass: 8399.360 Da / Num. of mol.: 1 / Fragment: residues 998-1071
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYO6, KIAA0389 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UM54

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C NOESY

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Sample preparation

DetailsContents: 0.7 mM [U-13C; U-15N] protein, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.7 mM / Component: entity-1 / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 50 / pH: 6.5 / Pressure: ambient / Temperature: 283 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE7002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
KUJIRANaohiro Kobayashichemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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