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- PDB-9fu2: Smooth Muscle Myosin II in complex with MT-228 -

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Basic information

Entry
Database: PDB / ID: 9fu2
TitleSmooth Muscle Myosin II in complex with MT-228
ComponentsMyosin-11
KeywordsMOTOR PROTEIN / Smooth Muscle Myosin II / MT-228 / myosin modulator / addiction / therapy / drug design
Function / homology
Function and homology information


elastic fiber assembly / skeletal muscle myosin thick filament assembly / muscle myosin complex / myosin filament / RHO GTPases Activate ROCKs / RHO GTPases activate CIT / actomyosin structure organization / Sema4D induced cell migration and growth-cone collapse / myosin II complex / cardiac muscle cell development ...elastic fiber assembly / skeletal muscle myosin thick filament assembly / muscle myosin complex / myosin filament / RHO GTPases Activate ROCKs / RHO GTPases activate CIT / actomyosin structure organization / Sema4D induced cell migration and growth-cone collapse / myosin II complex / cardiac muscle cell development / structural constituent of muscle / EPHA-mediated growth cone collapse / microfilament motor activity / RHO GTPases activate PAKs / smooth muscle contraction / Smooth Muscle Contraction / RHO GTPases activate PKNs / actin filament binding / melanosome / calmodulin binding / extracellular exosome / ATP binding / cytosol / cytoplasm
Similarity search - Function
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 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-11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.581 Å
AuthorsKikuti, C.M. / Houdusse, A.
Funding support France, United States, 4items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-21-Ce11-0022-01 France
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)R01DA049544 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R33NS119714 United States
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)UH3NS096833 United States
CitationJournal: To Be Published
Title: Development of clinically viable nonmuscle myosin II small molecule inhibitors
Authors: Radnai, L. / Young, E.J. / Kikuti, C.M. / Hafenbreidel, M. / Stremel, R. / Lin, L. / Toth, K. / Pasetto, P. / Jin, X. / Geedy, M. / Partridge, J. / Patel, A. / Conlon, M. / Briggs, S. / ...Authors: Radnai, L. / Young, E.J. / Kikuti, C.M. / Hafenbreidel, M. / Stremel, R. / Lin, L. / Toth, K. / Pasetto, P. / Jin, X. / Geedy, M. / Partridge, J. / Patel, A. / Conlon, M. / Briggs, S. / Sweeney, L.H. / Sellers, J. / Krieger-Burke, T. / Rumbaugh, G. / Cameron, M.D. / Surman, M. / Houdusse-Juille, A. / Griffin, P.R. / Kamenecka, T.M. / Miller, C.A.
History
DepositionJun 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 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-11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,26515
Polymers227,7191
Non-polymers1,54614
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-6 kcal/mol
Surface area32700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.106, 83.106, 132.251
Angle α, β, γ (deg.)90, 90, 120
Int Tables number144
Space group name H-MP31

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Myosin-11 / Myosin heavy chain 11 / Myosin heavy chain / smooth muscle isoform / SMMHC


Mass: 227718.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYH11, KIAA0866 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P35749

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Non-polymers , 8 types, 84 molecules

#2: 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
#3: Chemical ChemComp-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: VO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-A1IGE / (3~{a}~{S})-1-(2-methoxypyridin-4-yl)-6,7-dimethyl-3~{a}-oxidanyl-2,3-dihydropyrrolo[2,3-b]quinolin-4-one


Mass: 337.372 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H19N3O3 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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

Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 8.2 / Details: 10% PEG 3350; 50 mM Bicine pH 8.2 / Temp details: cold room

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid Nitrogen Stream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980089 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980089 Å / Relative weight: 1
ReflectionResolution: 2.581→71.97 Å / Num. obs: 30543 / % possible obs: 99.96 % / Redundancy: 1.6 % / Biso Wilson estimate: 62.92 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.05975 / Rpim(I) all: 0.05661 / Rrim(I) all: 0.08252 / Net I/σ(I): 5.31
Reflection shellResolution: 2.581→2.66 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.7954 / Mean I/σ(I) obs: 0.69 / Num. unique obs: 2620 / CC1/2: 0.369 / CC star: 0.734 / Rpim(I) all: 0.7704 / Rrim(I) all: 1.109 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSJan 10, 2022 (BUILT 20220820)data reduction
Aimless0.7.12data scaling
MOLREP11.9.02; 28.02.2022phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.581→71.97 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.925 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.433 / SU Rfree Blow DPI: 0.262
RfactorNum. reflection% reflectionSelection details
Rfree0.2497 1622 -RANDOM
Rwork0.2292 ---
obs0.2303 32160 100 %-
Displacement parametersBiso mean: 83.8 Å2
Baniso -1Baniso -2Baniso -3
1--4.0049 Å20 Å20 Å2
2---4.0049 Å20 Å2
3---8.0098 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: LAST / Resolution: 2.581→71.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5690 0 95 70 5855
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00711643HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8421030HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3515SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1844HARMONIC5
X-RAY DIFFRACTIONt_it5884HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion760SEMIHARMONIC5
X-RAY DIFFRACTIONt_utility_distance6HARMONIC1
X-RAY DIFFRACTIONt_utility_angle12HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact9249SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.17
X-RAY DIFFRACTIONt_other_torsion16.17
LS refinement shellResolution: 2.581→2.66 Å
RfactorNum. reflection% reflection
Rfree0.3709 39 -
Rwork0.3368 --
obs--100 %
Refinement TLS params.Origin x: -10.9882 Å / Origin y: 35.6003 Å / Origin z: 0.5712 Å
111213212223313233
T-0.1253 Å2-0.1036 Å2-0.0127 Å2-0.0114 Å2-0.016 Å2---0.1337 Å2
L1.8996 °2-1.0592 °2-1.1638 °2-1.3315 °20.9496 °2--1.6333 °2
S0.1559 Å °-0.0312 Å °-0.2626 Å °-0.0312 Å °0.1072 Å °0.3867 Å °-0.2626 Å °0.3867 Å °-0.2631 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A32 - 786
2X-RAY DIFFRACTION1{ A|* }A900 - 902
3X-RAY DIFFRACTION1{ A|* }A1001 - 1002
4X-RAY DIFFRACTION1{ A|* }A1003 - 1015

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