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- PDB-8qyp: Beta-cardiac myosin motor domain in the pre-powerstroke state -

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Basic information

Entry
Database: PDB / ID: 8qyp
TitleBeta-cardiac myosin motor domain in the pre-powerstroke state
ComponentsMyosin-7
KeywordsCONTRACTILE PROTEIN / cardiac myosin modulators inherited cardiomyopathies
Function / homology
Function and homology information


muscle filament sliding / myosin filament / myosin II complex / adult heart development / sarcomere organization / microfilament motor activity / myofibril / cardiac muscle contraction / sarcomere / actin filament binding ...muscle filament sliding / myosin filament / myosin II complex / adult heart development / sarcomere organization / microfilament motor activity / myofibril / cardiac muscle contraction / sarcomere / actin filament binding / calmodulin binding / ATP binding / cytoplasm
Similarity search - Function
DNA repair protein XRCC4-like, C-terminal / 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. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. ...DNA repair protein XRCC4-like, C-terminal / 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. / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / VANADATE ION / Myosin-7
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.759 Å
AuthorsRobert-Paganin, J. / Kikuti, C. / Auguin, D. / Rety, S. / David, A. / Houdusse, A.
Funding support France, United States, 4items
OrganizationGrant numberCountry
The French Muscular Dystrophy Telethon (AFM-Telethon)21805 France
Fondation pour la Recherche Medicale (FRM)DCM20181039553 France
Agence Nationale de la Recherche (ANR)21-CE11-0022-01 France
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RM1GM131981-01 United States
CitationJournal: Biorxiv / Year: 2023
Title: Omecamtiv mecarbil and Mavacamten target the same myosin pocket despite antagonistic effects in heart contraction.
Authors: Auguin, D. / Robert-Paganin, J. / Rety, S. / Kikuti, C. / David, A. / Theumer, G. / Schmidt, A.W. / Knolker, H.J. / Houdusse, A.
History
DepositionOct 26, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myosin-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6814
Polymers89,1151
Non-polymers5663
Water543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-23 kcal/mol
Surface area30650 Å2
Unit cell
Length a, b, c (Å)94.397, 94.397, 219.693
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein Myosin-7 / / Myosin heavy chain 7 / Myosin heavy chain slow isoform / MyHC-slow / Myosin heavy chain / cardiac ...Myosin heavy chain 7 / Myosin heavy chain slow isoform / MyHC-slow / Myosin heavy chain / cardiac muscle beta isoform / MyHC-beta


Mass: 89114.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q9BE39
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


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


Mass: 114.939 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: VO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
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

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.35 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.5M Lithium Sulfate 0.1M Tris-HCl 25% PEG 3350 2mM Mg.ADP.Vanadate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98007 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98007 Å / Relative weight: 1
ReflectionResolution: 2.759→94.4 Å / Num. obs: 20166 / % possible obs: 94.4 % / Redundancy: 25.9 % / Biso Wilson estimate: 79.62 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.273 / Net I/σ(I): 10.8
Reflection shellResolution: 2.759→3.033 Å / Rmerge(I) obs: 2.413 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1009 / CC1/2: 0.71 / % possible all: 64.2

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (18-SEP-2020)refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.759→94.4 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.9 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.393
RfactorNum. reflection% reflectionSelection details
Rfree0.2478 1011 5.01 %RANDOM
Rwork0.1897 ---
obs0.1926 20166 76.2 %-
Displacement parametersBiso mean: 77.73 Å2
Baniso -1Baniso -2Baniso -3
1-3.0114 Å20 Å20 Å2
2--3.0114 Å20 Å2
3----6.0228 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: LAST / Resolution: 2.759→94.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5663 0 57 3 5723
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0095838HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.027878HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2080SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes997HARMONIC5
X-RAY DIFFRACTIONt_it5838HARMONIC5
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.93
X-RAY DIFFRACTIONt_other_torsion20.66
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion753SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4912SEMIHARMONIC4
LS refinement shellResolution: 2.76→2.92 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2237 -4.95 %
Rwork0.2502 384 -
all0.249 404 -
obs--10.15 %
Refinement TLS params.Method: refined / Origin x: 15.8178 Å / Origin y: -35.4966 Å / Origin z: 16.2406 Å
111213212223313233
T-0.0147 Å2-0.1606 Å2-0.1271 Å2-0.048 Å20.1021 Å2---0.1057 Å2
L0.9181 °20.9907 °20.0493 °2-1.5187 °2-0.6053 °2--0.9023 °2
S0.363 Å °0.0298 Å °-0.0451 Å °0.2139 Å °-0.3732 Å °-0.1077 Å °0.051 Å °0.1733 Å °0.0102 Å °
Refinement TLS groupSelection details: { A|* }

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