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- PDB-3bz8: Crystal Structures of (S)-(-)-Blebbistatin Analogs bound to Dicty... -

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Basic information

Entry
Database: PDB / ID: 3bz8
TitleCrystal Structures of (S)-(-)-Blebbistatin Analogs bound to Dictyostelium discoideum myosin II
ComponentsMyosin-2 heavy chain, non muscle
KeywordsCONTRACTILE PROTEIN / myosin inhibitor / motor domain / blebbistatin analogue / Actin-binding / ATP-binding / Calmodulin-binding / Coiled coil / Cytoplasm / Methylation / Motor protein / Nucleotide-binding / Phosphoprotein
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
ADENOSINE-5'-DIPHOSPHATE / Chem-BL6 / VANADATE ION / Myosin-2 heavy chain
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsAllingham, J.S. / Rayment, I.
Citation
Journal: Org.Biomol.Chem. / Year: 2008
Title: The small molecule tool (S)-(-)-blebbistatin: novel insights of relevance to myosin inhibitor design.
Authors: Lucas-Lopez, C. / Allingham, J.S. / Lebl, T. / Lawson, C.P. / Brenk, R. / Sellers, J.R. / Rayment, I. / Westwood, N.J.
#1: Journal: 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
DepositionJan 17, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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.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.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myosin-2 heavy chain, non muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,6927
Polymers86,7471
Non-polymers9456
Water10,737596
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Myosin-2 heavy chain, non muscle
hetero molecules

A: Myosin-2 heavy chain, non muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,38514
Polymers173,4942
Non-polymers1,89012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area4340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.013, 147.772, 153.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Myosin-2 heavy chain, non muscle / Myosin II heavy chain / non muscle


Mass: 86747.109 Da / Num. of mol.: 1 / Fragment: Motor domain, Myosine head-like domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: mhcA / References: UniProt: P08799

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Non-polymers , 6 types, 602 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 / Vanadate


Mass: 114.939 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: VO4
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-BL6 / (3aS)-3a-hydroxy-7-methyl-1-phenyl-1,2,3,3a-tetrahydro-4H-pyrrolo[2,3-b]quinolin-4-one / S-3a-hydroxy-7-methyl-1-phenyl-1,2,3,3a-tetrahydro-4H-pyrrolo[2,3-b]quinolin-4-one


Mass: 292.332 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H16N2O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 596 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsAUTHOR STATES THAT THE LONG BOND DISTANCE IN VO4 REFLECTS THAT THIS VANADATE IS A TRANSITION STATE ...AUTHOR STATES THAT THE LONG BOND DISTANCE IN VO4 REFLECTS THAT THIS VANADATE IS A TRANSITION STATE ANALOG WITH BIPYRAMIDAL GEOMETRY.IN THESE COMPLEXES THE AXIAL V-O BOND DISTANCES ARE MUCH LONGER THAN SEEN IN SIMPLE VO4 COMPLEXES.
Sequence detailsTHE SEQUENCE CONFLICTS ARE DUE TO VARIATIONS OF DIFFERENT VERSIONS OF THE WILD-TYPE DICTYOSTELIUM MYOSIN.

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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: 2.87 Å3/Da / Density % sol: 57.18 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7
Details: mixing 5 ul of protein with an equal volume of well solution containing 100 mM MOPS, 250 mM MgCl2, 12% PEG 8000, 1 mM TCEP, and 2 mM Thymol, pH 7.0, 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: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 50629 / % possible obs: 99.1 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 10.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
2.2-2.284.50.22494.8
2.28-2.375.20.21298.5
2.37-2.485.80.18399.9
2.48-2.6160.146100
2.61-2.7760.11499.9
2.77-2.9960.09399.9
2.99-3.2960.07499.9
3.29-3.765.90.06399.9
3.76-4.745.90.0699.9
4.74-505.70.05898.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.425 / Cor.coef. Fo:Fc: 0.736
Highest resolutionLowest resolution
Rotation2.3 Å37.5 Å
Translation2.3 Å37.5 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1YV3

1yv3


Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.915 / SU B: 5.329 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.222 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24479 2569 5.1 %RANDOM
Rwork0.19224 ---
obs0.19493 48034 99.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.536 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å20 Å2
2--2.7 Å20 Å2
3----2.4 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5528 0 60 596 6184
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0225702
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8261.9597722
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2785708
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.68524.8275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.30715951
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4891528
X-RAY DIFFRACTIONr_chiral_restr0.1230.2848
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024349
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.22651
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.23899
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2070.2503
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.3230.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.246
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2990.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1471.53647
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.85525639
X-RAY DIFFRACTIONr_scbond_it2.81732389
X-RAY DIFFRACTIONr_scangle_it44.52081
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 167 -
Rwork0.234 3332 -
obs--93.91 %

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