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- PDB-6z7t: Nucleotide-free Myosin-II motor domain -

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Basic information

Entry
Database: PDB / ID: 6z7t
TitleNucleotide-free Myosin-II motor domain
ComponentsMyosin-2 heavy chain
KeywordsMOTOR PROTEIN / myosin / motorprotein / blebbistatin / ADP-release / inhibitor / complex / hydrolase
Function / homology
Function and homology information


calcium-dependent ATPase activity / pseudopodium retraction / 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 / RHO GTPases activate PAKs / contractile actin filament bundle assembly ...calcium-dependent ATPase activity / pseudopodium retraction / 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 / RHO GTPases activate PAKs / contractile actin filament bundle assembly / cell trailing edge / contractile vacuole organization / myosin filament assembly / aggregation involved in sorocarp development / culmination involved in sorocarp development / adenyl nucleotide binding / actomyosin contractile ring / hypotonic response / uropod / actin-myosin filament sliding / detection of mechanical stimulus / apical cortex / negative regulation of actin filament polymerization / bleb assembly / actomyosin / myosin filament / filopodium assembly / myosin II complex / early phagosome / microfilament motor activity / cortical actin cytoskeleton organization / cortical actin cytoskeleton / pseudopodium / cleavage furrow / cytoskeletal motor activity / mitotic cytokinesis / response to mechanical stimulus / response to cAMP / extracellular matrix / 14-3-3 protein binding / cell motility / response to hydrogen peroxide / protein localization / chemotaxis / actin filament binding / cell cortex / regulation of cell shape / cytoplasmic vesicle / cytoskeleton / calmodulin binding / ATP binding / identical protein 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. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. ...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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Myosin-2 heavy chain
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 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

Downloads & links

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Assembly

Deposited unit
A: Myosin-2 heavy chain
B: Myosin-2 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,54538
Polymers180,0292
Non-polymers2,51636
Water20,4471135
1
A: Myosin-2 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,14418
Polymers90,0151
Non-polymers1,13017
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Myosin-2 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,40120
Polymers90,0151
Non-polymers1,38619
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.681, 174.395, 100.252
Angle α, β, γ (deg.)90.000, 106.384, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 90014.562 Da / Num. of mol.: 2
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

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Non-polymers , 6 types, 1171 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1135 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.64 Å3/Da / Density % sol: 53.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 100 mM HEPES, pH7.5, 10% PEG8000, 8% Ethylenglycol

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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: 1.88→46.36 Å / Num. obs: 148819 / % possible obs: 98.7 % / Redundancy: 5.9 % / Biso Wilson estimate: 26.18 Å2 / CC1/2: 0.997 / Net I/σ(I): 9.46
Reflection shellResolution: 1.88→1.95 Å / Mean I/σ(I) obs: 1.81 / Num. unique obs: 14584 / CC1/2: 0.721

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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: 1.88→46.36 Å / SU ML: 0.2375 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.5946
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2167 3981 1.35 %
Rwork0.1907 290709 -
obs0.1911 148800 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.97 Å2
Refinement stepCycle: LAST / Resolution: 1.88→46.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11597 0 161 1135 12893
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.010812026
X-RAY DIFFRACTIONf_angle_d1.210716211
X-RAY DIFFRACTIONf_chiral_restr0.06091776
X-RAY DIFFRACTIONf_plane_restr0.00732124
X-RAY DIFFRACTIONf_dihedral_angle_d21.15391648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.90.32331440.33199861X-RAY DIFFRACTION94.08
1.9-1.930.3971360.306210308X-RAY DIFFRACTION97.83
1.93-1.950.33371420.292810432X-RAY DIFFRACTION97.9
1.95-1.980.27211340.267110164X-RAY DIFFRACTION97.86
1.98-2.010.26351470.252810435X-RAY DIFFRACTION98.03
2.01-2.040.23091400.254710308X-RAY DIFFRACTION98.01
2.04-2.070.32121420.251210254X-RAY DIFFRACTION98.12
2.07-2.10.27341420.244310451X-RAY DIFFRACTION98.24
2.1-2.140.25361440.230810330X-RAY DIFFRACTION98.27
2.14-2.180.2321440.224510479X-RAY DIFFRACTION98.49
2.18-2.220.26031350.214110182X-RAY DIFFRACTION98.48
2.22-2.270.21591500.203310523X-RAY DIFFRACTION98.69
2.27-2.320.21431400.194210327X-RAY DIFFRACTION98.59
2.32-2.370.23061420.1910448X-RAY DIFFRACTION98.58
2.37-2.430.2051420.182610343X-RAY DIFFRACTION98.74
2.43-2.50.2321400.188110401X-RAY DIFFRACTION98.93
2.5-2.570.25971440.189910498X-RAY DIFFRACTION98.61
2.57-2.650.19521390.180310364X-RAY DIFFRACTION99.17
2.65-2.750.19541440.177610404X-RAY DIFFRACTION98.96
2.75-2.860.22191450.179310538X-RAY DIFFRACTION99.04
2.86-2.990.23511420.180610412X-RAY DIFFRACTION99.24
2.99-3.140.1791400.178110479X-RAY DIFFRACTION99.22
3.14-3.340.1941400.169910512X-RAY DIFFRACTION99.38
3.34-3.60.19181440.164310409X-RAY DIFFRACTION99.26
3.6-3.960.19071440.167110390X-RAY DIFFRACTION99.08
3.96-4.530.19821460.15110503X-RAY DIFFRACTION99.52
4.53-5.710.18161450.167610488X-RAY DIFFRACTION99.44
5.71-48.090.21141440.215810466X-RAY DIFFRACTION99.3

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