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- PDB-6z2s: Crystal structure of adhibin analogue-bound myosin-2 -

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Basic information

Entry
Database: PDB / ID: 6z2s
TitleCrystal structure of adhibin analogue-bound myosin-2
ComponentsMyosin-2 heavy chain
KeywordsMOTOR PROTEIN / myosin / inhibitor / adhibin analogue / carbazole / pre-powerstroke state / 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
ACETATE ION / ADP METAVANADATE / 3,6-dibromo-1-(hydroxymethyl)carbazole / Myosin-2 heavy chain
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsEwert, W. / Knoelker, H.-J. / Tsiavaliaris, G. / Preller, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)PR 1478/2-1 Germany
CitationJournal: To Be Published
Title: The synthetic carbazole adhibin acts as selective myosin class-IX inhibitor in lung cancer cells
Authors: Bader, A. / Ewert, W. / Knoelker, H.-J. / Preller, M. / Tsiavaliaris, G.
History
DepositionMay 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,55912
Polymers90,0151
Non-polymers1,54411
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-12 kcal/mol
Surface area33680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.931, 144.220, 156.937
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-921-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 90014.562 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

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Non-polymers , 6 types, 36 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-Q5Q / 3,6-dibromo-1-(hydroxymethyl)carbazole / 3,4-bis(bromanyl)-6-methyl-9~{H}-carbazol-1-ol


Mass: 355.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H9Br2NO / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-AD9 / ADP METAVANADATE


Mass: 527.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P2V
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.86 Å3/Da / Density % sol: 56.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: 0.2 M lithium acetate and 20 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.979384 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979384 Å / Relative weight: 1
ReflectionResolution: 3.2→45.47 Å / Num. obs: 17402 / % possible obs: 99.87 % / Redundancy: 12.1 % / CC1/2: 0.996 / Net I/σ(I): 9.51
Reflection shellResolution: 3.2→3.31 Å / Num. unique obs: 1711 / CC1/2: 0.7

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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: 1vom

1vom


Resolution: 3.2→45.47 Å / SU ML: 0.4007 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.9148
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2621 775 4.46 %
Rwork0.2178 16615 -
obs0.2199 17390 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 82.93 Å2
Refinement stepCycle: LAST / Resolution: 3.2→45.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5769 0 91 25 5885
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00635967
X-RAY DIFFRACTIONf_angle_d0.71618095
X-RAY DIFFRACTIONf_chiral_restr0.0383904
X-RAY DIFFRACTIONf_plane_restr0.00251059
X-RAY DIFFRACTIONf_dihedral_angle_d22.9195812
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.40.36341160.27682743X-RAY DIFFRACTION99.97
3.4-3.660.29851100.2452754X-RAY DIFFRACTION99.93
3.66-4.030.26911320.21182726X-RAY DIFFRACTION99.93
4.03-4.610.23381120.19562766X-RAY DIFFRACTION99.97
4.61-5.810.24841470.20562765X-RAY DIFFRACTION99.93
5.81-45.470.25341580.21762861X-RAY DIFFRACTION99.77

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