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- PDB-5n69: Cardiac muscle myosin S1 fragment in the pre-powerstroke state co... -

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Basic information

Entry
Database: PDB / ID: 5n69
TitleCardiac muscle myosin S1 fragment in the pre-powerstroke state co-crystallized with the activator Omecamtiv Mecarbil
Components
  • Myosin light chain 3
  • Myosin-7
KeywordsMOTOR PROTEIN / myosin / cardiac / Omecamtiv Mecarbil / CK-452 / cytokinetics / 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 / calcium ion 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 / EF-hand / Recoverin; domain 1 / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-2OW / ADENOSINE-5'-DIPHOSPHATE / 3,3',3''-phosphanetriyltripropanoic acid / VANADATE ION / Myosin light chain 3 / Myosin-7
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsPlanelles-Herrero, V.J. / Hartman, J.J. / Robert-Paganin, J. / Malik, F.I. / Houdusse, A.
Funding support France, 6items
OrganizationGrant numberCountry
AFM18423 France
FRMDBI20141231319 France
French National Research Agency13-BSV8-0019-01 France
AFM17235 France
Labex CelTisPhyBio11-LBX-0038 France
IDEX PSLANR-10-IDEX-0001-02 PSL 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 16, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.content_type
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myosin-7
B: Myosin-7
G: Myosin light chain 3
H: Myosin light chain 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,09438
Polymers233,6064
Non-polymers4,48834
Water15,205844
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19020 Å2
ΔGint-113 kcal/mol
Surface area78920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.320, 122.450, 187.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules ABGH

#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: 94834.734 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q9BE39
#2: Protein Myosin light chain 3 / / Myosin light chain 1 / slow-twitch muscle B/ventricular isoform / MLC1SB


Mass: 21968.023 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P85100

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Non-polymers , 7 types, 878 molecules

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


Mass: 427.201 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: VO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-2OW / methyl 4-(2-fluoro-3-{[(6-methylpyridin-3-yl)carbamoyl]amino}benzyl)piperazine-1-carboxylate / omecamtiv mercarbil / Omecamtiv mecarbil


Mass: 401.435 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24FN5O3
#7: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-TCE / 3,3',3''-phosphanetriyltripropanoic acid / 3-[bis(2-carboxyethyl)phosphanyl]propanoic acid / TCEP


Mass: 250.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15O6P
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 844 / 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: 2.42 Å3/Da / Density % sol: 49.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 24% (w/v) PEG 3350, 5% Tacsimate pH 6.0, 5 mM TCEP, 20% Glycerol and 10% DMSO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 82998 / % possible obs: 99.3 % / Redundancy: 8.6 % / Biso Wilson estimate: 56.43 Å2 / CC1/2: 0.99 / Rsym value: 0.3 / Net I/σ(I): 5.41
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 8 % / Mean I/σ(I) obs: 0.96 / CC1/2: 0.38 / Rsym value: 1.73 / % possible all: 95.9

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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: 2.45→24.22 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.915 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.405 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.435 / SU Rfree Blow DPI: 0.241 / SU Rfree Cruickshank DPI: 0.241
RfactorNum. reflection% reflectionSelection details
Rfree0.224 4145 5 %RANDOM
Rwork0.18 ---
obs0.182 82903 99.1 %-
Displacement parametersBiso mean: 56.75 Å2
Baniso -1Baniso -2Baniso -3
1-9.7536 Å20 Å20 Å2
2--0.9096 Å20 Å2
3----10.6632 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: 1 / Resolution: 2.45→24.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14797 0 313 844 15954
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0115415HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1320715HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5607SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes429HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2185HARMONIC5
X-RAY DIFFRACTIONt_it15415HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.84
X-RAY DIFFRACTIONt_other_torsion19.87
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1958SEMIHARMONIC5
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_contact17379SEMIHARMONIC4
LS refinement shellResolution: 2.45→2.51 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 267 5 %
Rwork0.223 5073 -
all0.225 5340 -
obs--87.68 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.51910.2905-0.15460.4938-0.23290.50930.0817-0.07630.04340.0577-0.0478-0.0496-0.009-0.0495-0.03390.1718-0.0156-0.00230.2218-0.00640.1983-5.472-5.95741.195
20.62280.1928-0.01631.0751-0.05920.31910.03860.06090.04250.0106-0.04010.0340.0399-0.03340.00150.1989-0.013-0.02130.23990.02360.2381-33.703-19.73616.709
32.60022.62320.48319.3703-0.52882.8363-0.02240.1743-0.2986-0.0874-0.2089-0.5016-0.05220.11880.23130.4511-0.02910.00530.41940.06040.6205-33.306-72.36331.007
41.1870.9825-0.50912.2314-1.15961.5535-0.0027-0.0418-0.0902-0.0627-0.05090.04410.1198-0.12010.05360.29630.00840.02650.26110.04450.309616.58330.3246.482
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|4 - A|810 }
2X-RAY DIFFRACTION2{ B|5 - B|809 }
3X-RAY DIFFRACTION3{ G|41 - G|199 }
4X-RAY DIFFRACTION4{ H|39 - H|199 }

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