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- PDB-5n6a: Cardiac muscle myosin motor domain in the pre-powerstroke state -

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Basic information

Entry
Database: PDB / ID: 5n6a
TitleCardiac muscle myosin motor domain in the pre-powerstroke state
ComponentsMyosin-7
KeywordsMOTOR PROTEIN / myosin / cardiac / pre-powerstroke
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 / PHOSPHATE ION / Myosin-7
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsPlanelles-Herrero, V.J. / Hartman, J.J. / Robert-Paganin, J. / Malik, F.I. / Houdusse, A.
Funding support France, 5items
OrganizationGrant numberCountry
AFM18423 France
FRMDBI20141231319 France
French National Research Agency13-BSV8-0019-01 France
AFM17235 France
Ligue contre le cancerRS16 France
CitationJournal: Nat Commun / Year: 2017
Title: Mechanistic and structural basis for activation of cardiac myosin force production by omecamtiv mecarbil.
Authors: Planelles-Herrero, V.J. / Hartman, J.J. / Robert-Paganin, J. / Malik, F.I. / Houdusse, A.
History
DepositionFeb 14, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 17, 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

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Assembly

Deposited unit
A: Myosin-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,4315
Polymers94,7931
Non-polymers6394
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-29 kcal/mol
Surface area33870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.660, 149.830, 154.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1036-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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: 94792.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q9BE39

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Non-polymers , 5 types, 40 molecules

#2: 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
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

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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: 2.67 Å3/Da / Density % sol: 53.96 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 13% PEG 3350 (w/v), 5% Tacsimate pH 6.0, 5 mM TCEP, 10% Glycerol and 3.3% DMSO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9762 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 3.02→50 Å / Num. obs: 19862 / % possible obs: 98 % / Redundancy: 13.4 % / Biso Wilson estimate: 93.53 Å2 / CC1/2: 0.996 / Rsym value: 0.28 / Net I/σ(I): 8.35
Reflection shellResolution: 3.02→3.13 Å / Redundancy: 4 % / Mean I/σ(I) obs: 1.62 / CC1/2: 0.6 / Rsym value: 0.94 / % possible all: 80

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QVI

1qvi


Resolution: 3.1→43.83 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.843 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.527
RfactorNum. reflection% reflectionSelection details
Rfree0.32 940 5 %RANDOM
Rwork0.247 ---
obs0.25 18783 99.9 %-
Displacement parametersBiso mean: 85.53 Å2
Baniso -1Baniso -2Baniso -3
1-2.1364 Å20 Å20 Å2
2---0.7283 Å20 Å2
3----1.4081 Å2
Refine analyzeLuzzati coordinate error obs: 0.53 Å
Refinement stepCycle: 1 / Resolution: 3.1→43.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5485 0 39 36 5560
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015644HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.237635HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1928SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes148HARMONIC2
X-RAY DIFFRACTIONt_gen_planes830HARMONIC5
X-RAY DIFFRACTIONt_it5644HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.49
X-RAY DIFFRACTIONt_other_torsion24.31
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion750SEMIHARMONIC5
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_contact6469SEMIHARMONIC4
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0 / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.342 149 5 %
Rwork0.281 2830 -
all0.284 2979 -
obs--99.67 %
Refinement TLS params.Method: refined / Origin x: -22.6029 Å / Origin y: 37.9161 Å / Origin z: -29.4712 Å
111213212223313233
T-0.3047 Å2-0.0399 Å2-0.0092 Å2-0.4598 Å20.0762 Å2---0.2128 Å2
L0.9482 °20.3162 °20.0839 °2-1.0647 °20.553 °2--1.7968 °2
S0.0998 Å °-0.1512 Å °0.1351 Å °0.1301 Å °0.007 Å °0.1596 Å °0.0904 Å °-0.3065 Å °-0.1069 Å °
Refinement TLS groupSelection details: { A|* }

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