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- PDB-6z7u: Myosin-II motor domain complexed with blebbistatin in a new ADP-r... -

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Basic information

Entry
Database: PDB / ID: 6z7u
TitleMyosin-II motor domain complexed with blebbistatin in a new ADP-release conformation
ComponentsMyosin-2 heavy chain
KeywordsMOTOR PROTEIN / myosin / motorprotein / blebbistatin / ADP-release / inhibitor / complex / hydrolase
Function / homology
Function and homology information


uropod retraction / cytoplasmic actin-based contraction involved in forward cell motility / phagocytic cup base / pathogen-containing vacuole / response to differentiation-inducing factor 1 / equatorial cell cortex / contractile actin filament bundle assembly / pseudopodium retraction / cell trailing edge / contractile vacuole organization ...uropod retraction / cytoplasmic actin-based contraction involved in forward cell motility / phagocytic cup base / pathogen-containing vacuole / response to differentiation-inducing factor 1 / equatorial cell cortex / contractile actin filament bundle assembly / pseudopodium retraction / cell trailing edge / contractile vacuole organization / myosin filament assembly / aggregation involved in sorocarp development / culmination involved in sorocarp development / RHO GTPases activate PAKs / adenyl nucleotide binding / calcium-dependent ATPase activity / hypotonic response / actomyosin contractile ring / uropod / apical cortex / negative regulation of actin filament polymerization / detection of mechanical stimulus / actin-myosin filament sliding / substrate-dependent cell migration, cell extension / bleb assembly / actomyosin / filopodium assembly / myosin filament / early phagosome / myosin II complex / cortical actin cytoskeleton organization / cortical actin cytoskeleton / microfilament motor activity / pseudopodium / cleavage furrow / cytoskeletal motor activity / mitotic cytokinesis / response to cAMP / response to mechanical stimulus / 14-3-3 protein binding / extracellular matrix / cell motility / response to hydrogen peroxide / chemotaxis / actin filament binding / intracellular protein localization / regulation of cell shape / cytoplasmic vesicle / cell cortex / calmodulin binding / cytoskeleton / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #60 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #530 / 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 motor domain profile. / Myosin head, motor domain ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #60 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #530 / 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 motor domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin. Large ATPases. / IQ motif profile. / Kinesin motor domain superfamily / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chem-BIT / Myosin-2 heavy chain
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsEwert, W. / Preller, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)PR 1478/2-1 Germany
CitationJournal: Int J Mol Sci / Year: 2020
Title: Structural and Computational Insights into a Blebbistatin-Bound Myosin•ADP Complex with Characteristics of an ADP-Release Conformation along the Two-Step Myosin Power Stoke.
Authors: Ewert, W. / Franz, P. / Tsiavaliaris, G. / Preller, M.
History
DepositionJun 1, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myosin-2 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,00212
Polymers88,7241
Non-polymers1,27811
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint26 kcal/mol
Surface area32720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.373, 88.697, 199.891
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Myosin-2 heavy chain / Myosin II heavy chain


Mass: 88724.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: mhcA, DDB_G0286355 / Production host: Dictyostelium discoideum (eukaryote) / References: UniProt: P08799
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-BIT / (-)-1-PHENYL-1,2,3,4-TETRAHYDRO-4-HYDROXYPYRROLO[2,3-B]-7-METHYLQUINOLIN-4-ONE / (S)-BLEBBISTATIN / (3AS)-3A-HYDROXY-6-METHYL-1-PHENYL-3,3A-DIHYDRO-1H-PYRROLO[2,3-B]QUINOLIN-4(2H)-ONE


Mass: 292.332 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H16N2O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O
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: 2.37 Å3/Da / Density % sol: 48.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, pH7.5, 10% PEG8000, 8% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.58→46.1 Å / Num. obs: 27424 / % possible obs: 99.92 % / Redundancy: 13.2 % / Biso Wilson estimate: 44.78 Å2 / CC1/2: 0.998 / Net I/σ(I): 14.41
Reflection shellResolution: 2.58→2.67 Å / Mean I/σ(I) obs: 1.88 / Num. unique obs: 2669 / CC1/2: 0.754 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2aka

2aka


Resolution: 2.58→46.1 Å / SU ML: 0.3362 / Cross valid method: FREE R-VALUE / σ(F): 0.28 / Phase error: 26.598
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2309 2526 4.94 %
Rwork0.2002 48659 -
obs0.2018 27410 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.22 Å2
Refinement stepCycle: LAST / Resolution: 2.58→46.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5945 0 85 59 6089
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00596143
X-RAY DIFFRACTIONf_angle_d0.82338305
X-RAY DIFFRACTIONf_chiral_restr0.0498911
X-RAY DIFFRACTIONf_plane_restr0.00461088
X-RAY DIFFRACTIONf_dihedral_angle_d23.4006836
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.58-2.630.32181440.29732715X-RAY DIFFRACTION100
2.63-2.680.33251450.29252676X-RAY DIFFRACTION100
2.68-2.740.3391500.27952679X-RAY DIFFRACTION99.96
2.74-2.810.30791190.26612789X-RAY DIFFRACTION100
2.81-2.880.29321510.2712654X-RAY DIFFRACTION99.86
2.88-2.950.32351420.2562755X-RAY DIFFRACTION99.83
2.95-3.040.29161510.24832634X-RAY DIFFRACTION100
3.04-3.140.29741260.23362728X-RAY DIFFRACTION99.89
3.14-3.250.28831460.23722682X-RAY DIFFRACTION99.96
3.25-3.380.25581190.23552746X-RAY DIFFRACTION99.93
3.38-3.530.22371320.19542677X-RAY DIFFRACTION100
3.53-3.720.21241320.1912759X-RAY DIFFRACTION100
3.72-3.950.24531570.17392673X-RAY DIFFRACTION99.93
3.95-4.260.19161640.16092670X-RAY DIFFRACTION99.96
4.26-4.690.14831300.14752719X-RAY DIFFRACTION100
4.69-5.360.18551340.15832700X-RAY DIFFRACTION99.96
5.36-6.750.20961420.20352722X-RAY DIFFRACTION100
6.76-46.10.19371420.1772681X-RAY DIFFRACTION99.68

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