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- PDB-9htf: Beta-cardiac myosin Y115H mutant motor domain in the pre-powerstr... -

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Basic information

Entry
Database: PDB / ID: 9htf
TitleBeta-cardiac myosin Y115H mutant motor domain in the pre-powerstroke state, MgADP.VO4 form
ComponentsMyosin-7
KeywordsMOTOR PROTEIN / Cardiac myosin / Myosin II / muscle contraction / hypertrophic cardiomyopathy / thick filament / sarcomere
Function / homology
Function and homology information


regulation of slow-twitch skeletal muscle fiber contraction / regulation of the force of skeletal muscle contraction / muscle myosin complex / regulation of the force of heart contraction / transition between fast and slow fiber / myosin filament / adult heart development / cardiac muscle hypertrophy in response to stress / muscle filament sliding / myosin complex ...regulation of slow-twitch skeletal muscle fiber contraction / regulation of the force of skeletal muscle contraction / muscle myosin complex / regulation of the force of heart contraction / transition between fast and slow fiber / myosin filament / adult heart development / cardiac muscle hypertrophy in response to stress / muscle filament sliding / myosin complex / myosin II complex / ventricular cardiac muscle tissue morphogenesis / microfilament motor activity / myofibril / skeletal muscle contraction / striated muscle contraction / ATP metabolic process / cardiac muscle contraction / stress fiber / muscle contraction / regulation of heart rate / sarcomere / Z disc / 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. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / Myosin head, motor domain ...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. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.481 Å
AuthorsGlaser, C. / Houdusse, A.
Funding support France, United States, 6items
OrganizationGrant numberCountry
Fondation pour la Recherche Medicale (FRM)PBR202306017868 France
Laboratories of Excellence (LabEx)ANR-11-LBX-0038 France
IdEx Universite Paris CiteANR-10-IDEX-0001-02-PSL France
Centre National de la Recherche Scientifique (CNRS) France
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIH RM1 GM131981-01 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIH R01 GM033289 United States
CitationJournal: Nat Commun / Year: 2025
Title: Hypertrophic cardiomyopathy mutations Y115H and E497D disrupt the folded-back state of human beta-cardiac myosin allosterically.
Authors: Nandwani, N. / Bhowmik, D. / Glaser, C. / Childers, M.C. / Goluguri, R.R. / Dawood, A. / Regnier, M. / Houdusse, A. / Spudich, J.A. / Ruppel, K.M.
History
DepositionDec 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myosin-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,1397
Polymers93,3561
Non-polymers7836
Water1,29772
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-18 kcal/mol
Surface area30270 Å2
Unit cell
Length a, b, c (Å)93.553, 93.553, 220.48
Angle α, β, γ (deg.)90, 90, 90
Int Tables number95
Space group name H-MP4322

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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: 93355.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: Cardiac muscle / Gene: MYH7, MYHCB / Organ: Heart / Cell (production host): Myoblast / Cell line (production host): C2C12 / Organ (production host): Muscle / Production host: Mus musculus (house mouse) / Tissue (production host): Skeletal muscle / References: UniProt: P12883

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Non-polymers , 6 types, 78 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-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


Mass: 114.939 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: VO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.59 Å3/Da / Density % sol: 52.47 % / Description: Stick with a central longitudinal crack
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 23 % PEG 3350 w:v, 0.3 M lithium sulfate, 0.1M Tris-HCl, 2 mM 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: 0.98011 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.481→93.553 Å / Num. obs: 21395 / % possible obs: 60.1 % / Redundancy: 9.1 % / CC1/2: 0.991 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.06 / Rrim(I) all: 0.182 / Net I/σ(I): 8.4
Reflection shellResolution: 2.481→2.793 Å / Redundancy: 8.6 % / Rmerge(I) obs: 1.288 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1070 / CC1/2: 0.7 / Rpim(I) all: 0.461 / Rrim(I) all: 1.37 / % possible all: 10.3

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDS1.12.15data reduction
autoPROC1.0.5data scaling
MOLREP1.20.1-4487-000phasing
Coot0.9.8.92model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.481→93.553 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.902 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.383
RfactorNum. reflection% reflectionSelection details
Rfree0.2552 1033 4.83 %RANDOM
Rwork0.2071 ---
obs0.2094 21395 60.1 %-
Displacement parametersBiso mean: 71.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.8386 Å20 Å20 Å2
2--0.8386 Å20 Å2
3----1.6772 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: LAST / Resolution: 2.481→93.553 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5562 0 47 72 5681
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0075754HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.97762HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2036SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes976HARMONIC5
X-RAY DIFFRACTIONt_it5754HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion735SEMIHARMONIC5
X-RAY DIFFRACTIONt_utility_distance6HARMONIC1
X-RAY DIFFRACTIONt_utility_angle13HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact4543SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.66
X-RAY DIFFRACTIONt_other_torsion19.48
LS refinement shellResolution: 2.481→2.66 Å
RfactorNum. reflection% reflection
Rfree0.3341 25 5.84 %
Rwork0.273 428 -
obs--6.43 %
Refinement TLS params.Origin x: -31.7228 Å / Origin y: -11.6281 Å / Origin z: -16.9656 Å
111213212223313233
T-0.0626 Å20.1707 Å20.1352 Å2-0.0442 Å20.1209 Å2---0.0315 Å2
L1.0909 °2-1.1245 °2-0.2151 °2-1.6778 °2-0.5459 °2--1.3831 °2
S0.4075 Å °-0.1979 Å °-0.0003 Å °-0.1979 Å °-0.4152 Å °0.2555 Å °-0.0003 Å °0.2555 Å °0.0077 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ *|* }A30 - 781
2X-RAY DIFFRACTION1{ *|* }A800 - 807
3X-RAY DIFFRACTION1{ *|* }W1 - 74

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