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- PDB-6e5n: Solution structure of human Myosin VI isoform 3 (1050-1131) in co... -

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Basic information

Entry
Database: PDB / ID: 6e5n
TitleSolution structure of human Myosin VI isoform 3 (1050-1131) in complex with Clathrin light chain a (46-61)
Components
  • Clathrin light chain A
  • Unconventional myosin-VI
KeywordsMOTOR PROTEIN / Myosin / Clathrin / Trafficking / Endocytosis
Function / homology
Function and homology information


postsynaptic endocytic zone cytoplasmic component / regulation of secretion / clathrin vesicle coat / clathrin coat of trans-Golgi network vesicle / presynaptic endocytic zone membrane / clathrin complex / minus-end directed microfilament motor activity / clathrin coat / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / unconventional myosin complex ...postsynaptic endocytic zone cytoplasmic component / regulation of secretion / clathrin vesicle coat / clathrin coat of trans-Golgi network vesicle / presynaptic endocytic zone membrane / clathrin complex / minus-end directed microfilament motor activity / clathrin coat / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / unconventional myosin complex / Entry of Influenza Virion into Host Cell via Endocytosis / WNT5A-dependent internalization of FZD4 / clathrin heavy chain binding / clathrin coat of coated pit / LDL clearance / actin filament-based movement / inner ear auditory receptor cell differentiation / clathrin coat assembly / clathrin-coated vesicle membrane / Retrograde neurotrophin signalling / clathrin-coated endocytic vesicle / Formation of annular gap junctions / Gap junction degradation / clathrin-dependent endocytosis / endolysosome membrane / Trafficking of AMPA receptors / RHOBTB1 GTPase cycle / inner ear morphogenesis / Lysosome Vesicle Biogenesis / Golgi Associated Vesicle Biogenesis / microfilament motor activity / filamentous actin / Recycling pathway of L1 / cytoskeletal motor activity / microvillus / RHOU GTPase cycle / endocytic vesicle / DNA damage response, signal transduction by p53 class mediator / EPH-ephrin mediated repulsion of cells / RHOBTB2 GTPase cycle / clathrin-coated pit / ruffle / MHC class II antigen presentation / VLDLR internalisation and degradation / autophagosome / trans-Golgi network membrane / filopodium / actin filament organization / actin filament / intracellular protein transport / sensory perception of sound / peptide binding / ADP binding / ruffle membrane / synaptic vesicle membrane / spindle / endocytosis / actin filament binding / protein localization / actin cytoskeleton / Cargo recognition for clathrin-mediated endocytosis / apical part of cell / GTPase binding / Clathrin-mediated endocytosis / actin binding / cell cortex / cytoplasmic vesicle / nuclear membrane / calmodulin binding / endosome / response to xenobiotic stimulus / lysosomal membrane / cell division / protein-containing complex binding / perinuclear region of cytoplasm / structural molecule activity / Golgi apparatus / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Clathrin light chain / Clathrin light chain signature 1. / Clathrin light chain signature 2. / Clathrin light chain / Myosin VI, cargo binding domain / Class VI myosin, motor domain / : / Myosin VI cargo binding domain / Myosin VI, lever arm / Myosin S1 fragment, N-terminal ...Clathrin light chain / Clathrin light chain signature 1. / Clathrin light chain signature 2. / Clathrin light chain / 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
Clathrin light chain A / Unconventional myosin-VI
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsBuel, G.R. / Walters, K.J.
CitationJournal: Nat Commun / Year: 2019
Title: Clathrin light chain A drives selective myosin VI recruitment to clathrin-coated pits under membrane tension.
Authors: Biancospino, M. / Buel, G.R. / Nino, C.A. / Maspero, E. / Scotto di Perrotolo, R. / Raimondi, A. / Redlingshofer, L. / Weber, J. / Brodsky, F.M. / Walters, K.J. / Polo, S.
History
DepositionJul 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2020Group: 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
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3May 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
B: Unconventional myosin-VI
A: Clathrin light chain A


Theoretical massNumber of molelcules
Total (without water)12,3652
Polymers12,3652
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 300structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 9991.648 Da / Num. of mol.: 1
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
#2: Protein/peptide Clathrin light chain A / Lca


Mass: 2373.528 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLTA / Production host: Escherichia coli (E. coli) / References: UniProt: P09496

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D 1H-15N NOESY
131isotropic12D 1H-13C HSQC
141isotropic13D 1H-13C NOESY
152isotropic12D 1H-15N HSQC
192isotropic13D 1H-15N NOESY
182isotropic12D 1H-13C HSQC
172isotropic13D 1H-13C NOESY
161isotropic23D HNCO
1101isotropic13D HN(CA)CB
1122isotropic13D HNCO
1112isotropic13D HN(CA)CB
1131isotropic1half-filtered 3D 1H-13C NOESY
1142isotropic1half-filtered 3D 1H-13C NOESY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution10.36 mM [U-13C; U-15N] Myosin VI 1050-1131, 0.36 mM None Clathrin Light Chain Alpha 46-61, 95% H2O/5% D2OAn additional 5 non-native amino acids from the vector are present at the N-terminal end of the Myosin VI construct. These are GPLGS. An additional 8 non-native amino acids from the vector are present at the N-terminal end of the Clathrin construct. These are GPLGSPEF. These are intrinsically disordered and not included in the structure calculations.CLCa_13C-15N-Myo695% H2O/5% D2O
solution20.4 mM None Myosin VI 1050-1131, 0.4 mM [U-13C; U-15N] Clathrin Light Chain Alpha 46-61, 95% H2O/5% D2OAn additional 5 non-native amino acids from the vector are present at the N-terminal end of the Myosin VI construct. These are GPLGS. An additional 8 non-native amino acids from the vector are present at the N-terminal end of the Clathrin construct. These are GPLGSPEF. These are intrinsically disordered and not included in the structure calculations.Myo6_13C-15N-CLCa95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.36 mMMyosin VI 1050-1131[U-13C; U-15N]1
0.36 mMClathrin Light Chain Alpha 46-61None1
0.4 mMMyosin VI 1050-1131None2
0.4 mMClathrin Light Chain Alpha 46-61[U-13C; U-15N]2
Sample conditionsIonic strength: 50 mM NaCl, 20 mM NaPO4 mM / Label: Conditions_all / pH: 6.5 / Pressure: 760 mmHg / Temperature: 283.2 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III8501
Bruker AVANCE IIIBrukerAVANCE III7002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASYBartels et al.peak picking
XEASYBartels et al.chemical shift assignment
TALOSCornilescu, Delaglio and Baxgeometry optimization
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 8
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 300 / Conformers submitted total number: 20

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