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- PDB-6ysy: Skeletal Myosin bound to MPH-220, MgADP-VO4 -

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Basic information

Entry
Database: PDB / ID: 6ysy
TitleSkeletal Myosin bound to MPH-220, MgADP-VO4
Components
  • Myosin light chain 1/3, skeletal muscle isoform
  • Myosin-4
KeywordsMOTOR PROTEIN / myofibril / muscle spasticity / actin binding / inhibitor
Function / homology
Function and homology information


myosin filament / myosin complex / structural constituent of muscle / myofibril / cytoskeletal motor activity / actin filament binding / calmodulin binding / calcium ion binding / ATP binding
Similarity search - Function
: / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / Myosin head, motor domain / Myosin head (motor domain) ...: / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / IQ motif, EF-hand binding site / Kinesin motor domain superfamily / EF-hand, calcium binding motif / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chem-PJT / VANADATE ION / Myosin light chain 1/3, skeletal muscle isoform / Myosin-4
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.246 Å
AuthorsCanon, L. / Kikuti, C.M. / Gyimesi, M. / Malnasi-Csizmadia, A. / Houdusse, A.
Funding support Hungary, France, 10items
OrganizationGrant numberCountry
Hungarian National Research, Development and Innovation OfficeNVKP 16-1-2016-0051 Hungary
Hungarian Ministry of FinanceGINOP-2.1.7-15-2016-02580 Hungary
Hungarian Ministry of FinanceGINOP 2.3.2-15-2016-00016 Hungary
French League Against CancerIP/SC-16058 France
Centre National de la Recherche Scientifique (CNRS) France
Foundation for Medical Research (France)DCM20181039553 France
French National Research AgencyANR-17-CE11-0029-01 France
French Muscular Dystrophy AssociationAFM 21805 France
French National Research AgencyANR-10-IDEX-0001-02-PSL France
Laboratories of Excellence (LabEx)11-LBX-0038 France
CitationJournal: Cell / Year: 2020
Title: Single Residue Variation in Skeletal Muscle Myosin Enables Direct and Selective Drug Targeting for Spasticity and Muscle Stiffness.
Authors: Gyimesi, M. / Horvath, A.I. / Turos, D. / Suthar, S.K. / Penzes, M. / Kurdi, C. / Canon, L. / Kikuti, C. / Ruppel, K.M. / Trivedi, D.V. / Spudich, J.A. / Lorincz, I. / Rauscher, A.A. / ...Authors: Gyimesi, M. / Horvath, A.I. / Turos, D. / Suthar, S.K. / Penzes, M. / Kurdi, C. / Canon, L. / Kikuti, C. / Ruppel, K.M. / Trivedi, D.V. / Spudich, J.A. / Lorincz, I. / Rauscher, A.A. / Kovacs, M. / Pal, E. / Komoly, S. / Houdusse, A. / Malnasi-Csizmadia, A.
History
DepositionApr 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myosin-4
B: Myosin light chain 1/3, skeletal muscle isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,4106
Polymers244,4602
Non-polymers9504
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-45 kcal/mol
Surface area41440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.607, 119.424, 176.631
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Myosin-4 / / Myosin heavy chain 2b / MyHC-2b / Myosin heavy chain 4 / Myosin heavy chain / skeletal muscle / juvenile


Mass: 223485.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: Skeletal muscle / References: UniProt: Q28641
#2: Protein Myosin light chain 1/3, skeletal muscle isoform / MLC1F/MLC3F / Myosin light chain alkali 1/2 / Myosin light chain A1/A2


Mass: 20974.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: Skeletal muscle / References: UniProt: P02602

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Non-polymers , 5 types, 36 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-VO4 / VANADATE ION / Vanadate


Mass: 114.939 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: VO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-PJT / (9~{S})-5-methyl-12-(4-morpholin-4-ylphenyl)-9-oxidanyl-4-thia-2,12-diazatricyclo[7.3.0.0^{3,7}]dodeca-1,3(7),5-trien-8-one


Mass: 383.464 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H21N3O3S / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 35% PEG600, 20mM DTT; 100mM HEPES pH 7.0; 5% DMSO

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980102 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 6, 2020
Details: Cryogenically cooled channel cut crystal monochromator, a convex prefocussing mirror and a Kirkpatrick-Baez pair of focussing mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980102 Å / Relative weight: 1
ReflectionResolution: 3.246→98.93 Å / Num. obs: 17314 / % possible obs: 99.8 % / Redundancy: 2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.003722 / Net I/σ(I): 10.46
Reflection shellResolution: 3.246→3.4 Å / Rmerge(I) obs: 0.2293 / Num. unique obs: 1687 / CC1/2: 0.939 / % possible all: 99.88

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (6-FEB-2020)refinement
XDSdata reduction
autoPROCdata scaling
MOLREPphasing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1qvi

1qvi


Resolution: 3.246→98.93 Å / Cor.coef. Fo:Fc: 0.838 / Cor.coef. Fo:Fc free: 0.845 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.489
RfactorNum. reflection% reflectionSelection details
Rfree0.2323 854 -RANDOM
Rwork0.2175 ---
obs0.2183 17314 99.9 %-
Displacement parametersBiso mean: 100.13 Å2
Baniso -1Baniso -2Baniso -3
1--78.9127 Å20 Å20 Å2
2--29.839 Å20 Å2
3---49.0737 Å2
Refine analyzeLuzzati coordinate error obs: 0.51 Å
Refinement stepCycle: LAST / Resolution: 3.246→98.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7377 0 60 32 7469
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0097592HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0210244HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2729SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1318HARMONIC5
X-RAY DIFFRACTIONt_it7592HARMONIC5
X-RAY DIFFRACTIONt_chiral_improper_torsion981SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact5666SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.72
X-RAY DIFFRACTIONt_other_torsion18.31
LS refinement shellResolution: 3.25→3.27 Å
RfactorNum. reflection% reflection
Rfree0.34 17 -
Rwork0.2927 --
obs0.2951 413 99.28 %

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