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- PDB-6obi: Remarkable rigidity of the single alpha-helical domain of myosin-... -

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Basic information

Entry
Database: PDB / ID: 6obi
TitleRemarkable rigidity of the single alpha-helical domain of myosin-VI revealed by NMR spectroscopy
ComponentsMyosin-VI
KeywordsMOTOR PROTEIN / myosin-VI / alpha-helical domain
Function / homologyMyosin-VI
Function and homology information
Biological speciesMeriones unguiculatus (Mongolian gerbil)
MethodSOLUTION NMR / simulated annealing
AuthorsBarnes, A. / Shen, Y. / Ying, J. / Takagi, Y. / Torchia, D.A. / Sellers, J. / Bax, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)the Intramural Research Program United States
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: Remarkable Rigidity of the Single alpha-Helical Domain of Myosin-VI As Revealed by NMR Spectroscopy.
Authors: Barnes, C.A. / Shen, Y. / Ying, J. / Takagi, Y. / Torchia, D.A. / Sellers, J.R. / Bax, A.
History
DepositionMar 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jun 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 1.4May 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)8,9401
Polymers8,9401
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Myosin-VI


Mass: 8939.936 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Meriones unguiculatus (Mongolian gerbil)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A5H1ZR50*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
121isotropic1TROSY-HSQC
111isotropic14D 1H-15N-15N-1H HMQC-NOESY-TROSY-HSQC
131isotropic13D TROSY-HN(CA)CB
142isotropic1ARTSY-J
252isotropic1WEX-III TROSY
361anisotropic1ARTSY
5111anisotropic1ARTSY
371anisotropic1E.COSY-HSQC-TROSY
483anisotropic1ARTSY
192isotropic2Heteronuclear TROSY-based relaxation
1102isotropic3Heteronuclear TROSY-based relaxation

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM U-15N; U-13-; U-2H 15N-, 13C-, and 2H-isotopically enriched, 100% D2O15N-, 13C-, and 2H-isotopically enriched100% D2O
solution21 mM U-15N; U-2H 15N-, and 2H-isotopically enriched, 100% D2O15N-, and 2H-isotopically enriched100% D2O
solution31 mM U-15N; U-13-; U-2H I13C MT-DOTA-Lu/Tm, 100% D2OI13C MT-DOTA-Lu/Tm100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mM15N-, 13C-, and 2H-isotopically enrichedU-15N; U-13-; U-2H1
1 mM15N-, and 2H-isotopically enrichedU-15N; U-2H2
1 mMI13C MT-DOTA-Lu/TmU-15N; U-13-; U-2H3
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)Details
120 mM2H-isotopically enriched sample6.31 bar293 K
225 mMpH 7.8 for HX rates measurement7.81 bar293 K1-mM sample of perdeuterated, 15N-enriched MT sample in 95% H2O, 5% D2O, 25 mM sodium phosphate buffer, pH 7.8
325 mMpf1 sample6.31 bar293 K13 mg/mL Pf1 in 25 mM sodium phosphate buffer, pH 6.3, 2 mM EDTA
5100 mMpf1 sample (high salt)6.31 bar293 K13 mg/mL Pf1 in 25 mM sodium phosphate buffer, pH 6.3, 2 mM EDTA, an additional 100 mM NaCl
425 mMTm/Lu lanthanide aligned sample6.31 bar293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker 900 MHz Bruker Avance IIBruker900 MHz Bruker Avance II9001
Bruker 800 MHz BrukerBruker800 MHz Bruker8002
Bruker 600 MHz BrukerBruker600 MHz Bruker6003

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 10

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