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- PDB-9i8p: Human beta-cardiac myosin wild type motor domain in the pre-power... -

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Basic information

Entry
Database: PDB / ID: 9i8p
TitleHuman beta-cardiac myosin wild type 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: 2.601 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
DepositionFeb 5, 2025Deposition 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)94,3569
Polymers93,3811
Non-polymers9758
Water1,27971
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-38 kcal/mol
Surface area32060 Å2
Unit cell
Length a, b, c (Å)93.935, 93.935, 219.678
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: 93380.984 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 , 7 types, 79 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.6 Å3/Da / Density % sol: 52.7 % / Description: Stick with a central longitudinal crack
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 25 % PEG 3350 w:v, 0.25 M lithium sulfate, 0.1M Tris-HCl, 2 mM Mg.ADP.Vanadate. Optimal crystals were obtained using the micro-seeding technique.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 20, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.601→19.899 Å / Num. obs: 21409 / % possible obs: 69.1 % / Redundancy: 26.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.319 / Rpim(I) all: 0.062 / Rrim(I) all: 0.325 / Net I/σ(I): 10.8
Reflection shellResolution: 2.601→2.85 Å / Redundancy: 26.2 % / Rmerge(I) obs: 2.32 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1070 / CC1/2: 0.738 / Rpim(I) all: 0.459 / Rrim(I) all: 2.366 / % possible all: 14.6

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDS1.12.15data reduction
autoPROC1.0.5data scaling
MOLREP1.21.2-5419-000phasing
Coot0.9.8.95model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.601→19.899 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.899 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.372
RfactorNum. reflection% reflectionSelection details
Rfree0.2455 1060 4.95 %RANDOM
Rwork0.2057 ---
obs0.2077 21409 69.1 %-
Displacement parametersBiso mean: 61.45 Å2
Baniso -1Baniso -2Baniso -3
1-3.0822 Å20 Å20 Å2
2--3.0822 Å20 Å2
3----6.1645 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: LAST / Resolution: 2.601→19.899 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5679 0 57 71 5807
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0075863HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.897907HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2065SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes989HARMONIC5
X-RAY DIFFRACTIONt_it5863HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion752SEMIHARMONIC5
X-RAY DIFFRACTIONt_utility_distance6HARMONIC1
X-RAY DIFFRACTIONt_utility_angle13HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact4654SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.55
X-RAY DIFFRACTIONt_other_torsion19.09
LS refinement shellResolution: 2.601→2.73 Å
RfactorNum. reflection% reflection
Rfree0.44 17 3.96 %
Rwork0.2776 429 -
obs--10.76 %
Refinement TLS params.Origin x: 15.173 Å / Origin y: 35.4262 Å / Origin z: -16.6513 Å
111213212223313233
T-0.0861 Å20.1559 Å20.1475 Å2-0.0725 Å20.1218 Å2---0.0991 Å2
L1.1932 °2-1.0998 °2-0.2082 °2-1.7868 °2-0.4964 °2--1.7277 °2
S0.3827 Å °-0.3202 Å °-0.0068 Å °-0.3202 Å °-0.3784 Å °0.2298 Å °-0.0068 Å °0.2298 Å °-0.0043 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A30 - 780
2X-RAY DIFFRACTION1{ A|* }A800 - 808

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