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- PDB-8qyq: Beta-cardiac myosin S1 fragment in the pre-powerstroke state comp... -

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Basic information

Entry
Database: PDB / ID: 8qyq
TitleBeta-cardiac myosin S1 fragment in the pre-powerstroke state complexed to Mavacamten
Components
  • (Myosin light chain ...) x 2
  • Myosin-7
KeywordsCONTRACTILE PROTEIN / cardiac myosin modulators inherited cardiomyopathies mavcamten
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 calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / FORMIC ACID / Chem-XB2 / Myosin light chain 3 / Myosin-7
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 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
B: Myosin-7
C: Myosin light chain 3
D: Myosin light chain 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,50618
Polymers228,6024
Non-polymers1,90414
Water8,737485
1
A: Myosin-7
C: Myosin light chain 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,32310
Polymers114,3022
Non-polymers1,0218
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-34 kcal/mol
Surface area41850 Å2
MethodPISA
2
B: Myosin-7
D: Myosin light chain 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,1838
Polymers114,3002
Non-polymers8836
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-27 kcal/mol
Surface area37570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.801, 147.977, 116.751
Angle α, β, γ (deg.)90.00, 91.62, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Myosin-7 /


Mass: 92333.789 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q9BE39

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Myosin light chain ... , 2 types, 2 molecules CD

#2: Protein Myosin light chain 3 / / Myosin light chain 1 / slow-twitch muscle B/ventricular isoform / MLC1SB


Mass: 21968.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P85100
#3: Protein Myosin light chain 3 /


Mass: 21966.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P85100

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Non-polymers , 7 types, 499 molecules

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


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BeF3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-XB2 / 6-[[(1~{S})-1-phenylethyl]amino]-3-propan-2-yl-1~{H}-pyrimidine-2,4-dione


Mass: 273.330 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C15H19N3O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#9: 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
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 485 / 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

CrystalDensity Matthews: 4.34 Å3/Da / Density % sol: 71.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 5mM Mg.ADP.BeFx 5mM Mavacamten 20.5% PEG 3350 7.5% Na Tacsimate 5mM TCEP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.984 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.607→91.64 Å / Num. obs: 69889 / % possible obs: 93.6 % / Redundancy: 4.5 % / Biso Wilson estimate: 61.92 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.2 / Net I/σ(I): 7.4
Reflection shellResolution: 2.607→2.859 Å / Redundancy: 5.3 % / Rmerge(I) obs: 1.212 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3494 / CC1/2: 0.476 / % possible all: 61.2

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.61→91.64 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.901 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.654 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.607 / SU Rfree Blow DPI: 0.293 / SU Rfree Cruickshank DPI: 0.3
RfactorNum. reflection% reflectionSelection details
Rfree0.217 3478 4.98 %RANDOM
Rwork0.178 ---
obs0.18 69881 66 %-
Displacement parametersBiso mean: 63.44 Å2
Baniso -1Baniso -2Baniso -3
1--3.57 Å20 Å2-1.9547 Å2
2--6.4543 Å20 Å2
3----2.8844 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 2.61→91.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14285 0 173 485 14943
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0114798HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1519940HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5310SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes410HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2131HARMONIC5
X-RAY DIFFRACTIONt_it14798HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.83
X-RAY DIFFRACTIONt_other_torsion20.13
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1894SEMIHARMONIC5
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_contact17175SEMIHARMONIC4
LS refinement shellResolution: 2.61→2.68 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.161 -4.24 %
Rwork0.261 271 -
all0.256 283 -
obs--3.66 %
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)
10.47290.0012-0.18711.8597-1.40471.6403-0.00270.037-0.013-0.1085-0.02480.03110.1082-0.09170.0275-0.2387-0.0005-0.0473-0.0586-0.0973-0.2421-11.658822.17294.4685
22.27350.04350.25420.4299-0.16430.6645-0.0148-0.0404-0.12750.0210.0204-0.09140.05110.0892-0.0055-0.1772-0.0126-0.0213-0.1116-0.0259-0.159541.5513-19.236728.3322
30.6969-0.9279-1.31692.75462.81937.97750.0728-0.19620.11970.5095-0.15-0.1212-0.3081-0.30560.0772-0.07970.0085-0.08090.1546-0.1561-0.3271-11.483111.118158.217
42.50261.3998-1.43966.3161.36557.88620.1461-0.59820.0260.47520.06380.26910.1124-0.0844-0.20990.1293-0.11870.03730.18790.2293-0.564766.0352-20.869368.0321
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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