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- PDB-1yv3: The structural basis of blebbistatin inhibition and specificity f... -

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Basic information

Entry
Database: PDB / ID: 1yv3
TitleThe structural basis of blebbistatin inhibition and specificity for myosin II
ComponentsMyosin II heavy chain
KeywordsCONTRACTILE PROTEIN / myosin / blebbistatin / myosin II inhibitor / myosin-inhibitor complex / metastable state
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 / equatorial cell cortex / contractile actin filament bundle assembly / cell trailing edge / contractile vacuole organization ...calcium-dependent ATPase activity / pseudopodium retraction / uropod retraction / cytoplasmic actin-based contraction involved in forward cell motility / phagocytic cup base / pathogen-containing vacuole / equatorial cell cortex / contractile actin filament bundle assembly / 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 / response to differentiation-inducing factor 1 / hypotonic response / uropod / mitotic actomyosin contractile ring / actomyosin contractile ring / mitotic actomyosin contractile ring contraction / actin-myosin filament sliding / detection of mechanical stimulus / apical cortex / negative regulation of actin filament polymerization / bleb assembly / actomyosin / substrate-dependent cell migration, cell extension / myosin filament / filopodium assembly / early phagosome / cortical actin cytoskeleton organization / myosin II complex / cortical actin cytoskeleton / microfilament motor activity / pseudopodium / cytoskeletal motor activity / cleavage furrow / mitotic cytokinesis / response to mechanical stimulus / 14-3-3 protein binding / response to cAMP / extracellular matrix / muscle contraction / 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 / cytoplasm / cytosol
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
ADENOSINE-5'-DIPHOSPHATE / Chem-BIT / VANADATE ION / Myosin-2 heavy chain
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAllingham, J.S. / Smith, R. / Rayment, I.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2005
Title: The structural basis of blebbistatin inhibition and specificity for myosin II.
Authors: Allingham, J.S. / Smith, R. / Rayment, I.
History
DepositionFeb 14, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE The sequence conflicts are due to variations of different versions of the wild-type ...SEQUENCE The sequence conflicts are due to variations of different versions of the wild-type Dictyostelium myosin.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myosin II heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,6927
Polymers86,7471
Non-polymers9456
Water12,214678
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.106, 145.770, 152.912
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1679-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Myosin II heavy chain


Mass: 86747.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dictyostelium discoideum (eukaryote) / References: UniProt: P08799

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Non-polymers , 6 types, 684 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: VO4
#4: 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
#5: 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 / Comment: inhibitor*YM
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 678 / Source method: isolated from a natural source / Formula: H2O

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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: 2.82 Å3/Da / Density % sol: 56.01 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM MOPS (pH 7.0), 250 mM MgCl2, 11% PEG 8000, 1 mM TCEP, 2 mM Thymol, 1 mM MgCl2, 2 mM ADP, and 3 mM sodium vanadate, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 0.708 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 9, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.708 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 63478 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 33.4 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 24
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 3.7 / Num. unique all: 63478 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1VOM

1vom


Resolution: 2→40 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.839 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.141 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21498 3388 5.1 %RANDOM
Rwork0.17298 ---
all0.17514 ---
obs0.17514 63478 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.417 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å20 Å2
2--0.51 Å20 Å2
3----0.8 Å2
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5481 0 60 678 6219
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0215654
X-RAY DIFFRACTIONr_bond_other_d0.0020.025011
X-RAY DIFFRACTIONr_angle_refined_deg1.6851.9547656
X-RAY DIFFRACTIONr_angle_other_deg1.07311611
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9285701
X-RAY DIFFRACTIONr_chiral_restr0.1160.2846
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.026322
X-RAY DIFFRACTIONr_gen_planes_other0.0130.021159
X-RAY DIFFRACTIONr_nbd_refined0.2260.21137
X-RAY DIFFRACTIONr_nbd_other0.2480.25813
X-RAY DIFFRACTIONr_nbtor_other0.0890.23171
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2421
X-RAY DIFFRACTIONr_metal_ion_refined0.250.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1260.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3260.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2050.225
X-RAY DIFFRACTIONr_mcbond_it1.1741.53491
X-RAY DIFFRACTIONr_mcangle_it2.07225605
X-RAY DIFFRACTIONr_scbond_it3.05932163
X-RAY DIFFRACTIONr_scangle_it4.7564.52048
LS refinement shellResolution: 2→2.046 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.298 221
Rwork0.256 4463

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