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- PDB-2n10: Solution structure of MyUb (1080-1131) of human Myosin VI -

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Entry
Database: PDB / ID: 2n10
TitleSolution structure of MyUb (1080-1131) of human Myosin VI
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 / Trafficking of AMPA receptors / RHOBTB1 GTPase cycle / inner ear morphogenesis ...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 / Trafficking of AMPA receptors / RHOBTB1 GTPase cycle / inner ear morphogenesis / microfilament motor activity / filamentous actin / cytoskeletal motor activity / microvillus / RHOU GTPase cycle / endocytic vesicle / DNA damage response, signal transduction by p53 class mediator / RHOBTB2 GTPase cycle / clathrin-coated pit / ruffle / autophagosome / filopodium / actin filament organization / actin filament / intracellular protein transport / sensory perception of sound / ADP binding / ruffle membrane / endocytosis / actin filament binding / protein localization / 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 / cytosol / cytoplasm
Similarity search - Function
Myosin VI, cargo binding domain / Class VI myosin, motor domain / : / Myosin VI cargo binding domain / Myosin VI, lever arm / 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, cargo binding domain / Class VI myosin, motor domain / : / Myosin VI cargo binding domain / Myosin VI, lever arm / 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. / Ehlinger, A. / Walters, K.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA136472 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)1ZIABC011627 United States
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: RCSB / 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 1.3Apr 27, 2016Group: Structure summary
Revision 1.4Oct 13, 2021Group: Data collection / Database references
Category: database_2 / 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_nmr_software.name / _struct_ref_seq_dif.details
Revision 2.0Oct 20, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Experimental preparation / Other / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / entity_src_gen ...atom_site / entity_src_gen / pdbx_audit_support / pdbx_database_related / pdbx_database_status / pdbx_nmr_ensemble / pdbx_nmr_exptl / pdbx_nmr_exptl_sample / pdbx_nmr_exptl_sample_conditions / pdbx_nmr_refine / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_torsion / struct / struct_conf
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num ..._entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_seq_type / _pdbx_database_status.SG_entry / _pdbx_database_status.deposit_site / _pdbx_nmr_ensemble.conformer_selection_criteria / _pdbx_nmr_ensemble.conformers_calculated_total_number / _pdbx_nmr_exptl.sample_state / _pdbx_nmr_exptl.spectrometer_id / _pdbx_nmr_exptl_sample.component / _pdbx_nmr_exptl_sample_conditions.ionic_strength_units / _pdbx_nmr_exptl_sample_conditions.label / _pdbx_nmr_exptl_sample_conditions.pH_units / _pdbx_nmr_refine.software_ordinal / _pdbx_nmr_sample_details.contents / _pdbx_nmr_sample_details.label / _pdbx_nmr_sample_details.type / _pdbx_nmr_software.classification / _pdbx_nmr_spectrometer.type / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _struct.pdbx_CASP_flag / _struct_conf.pdbx_PDB_helix_id
Description: Atoms with unrealistic or zero occupancies / Provider: author / Type: Coordinate replacement
Revision 2.1Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 2.2May 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: Unconventional myosin-VI


Theoretical massNumber of molelcules
Total (without water)7,0551
Polymers7,0551
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 / 98structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 7055.110 Da / Num. of mol.: 1 / Fragment: residues 1080-1131
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-IDSample stateSpectrometer-IDType
111isotropic13D 1H-15N NOESY
121isotropic13D 1H-13C NOESY aliphatic
131isotropic13D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: solution
Contents: 0.7 mM [U-13C; U-15N] Unconventional myosin-VI, 90% H2O/10% D2O
Label: sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.7 mM / Component: Unconventional myosin-VI / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 50 mM / Label: condition / pH: 6.5 / Pressure: ambient / Temperature: 283 K

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NMR measurement

NMR spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 900 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
KUJIRANaohiro Kobayashichemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 98 / Conformers submitted total number: 20

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