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- PDB-3myh: Insights into the Importance of Hydrogen Bonding in the Gamma-Pho... -

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Basic information

Entry
Database: PDB / ID: 3myh
TitleInsights into the Importance of Hydrogen Bonding in the Gamma-Phosphate Binding Pocket of Myosin: Structural and Functional Studies of Ser236
ComponentsMyosin-2 heavy chain
KeywordsSTRUCTURAL PROTEIN / S1dc / myosin / S236A
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 / contractile actin filament bundle assembly / cell trailing edge ...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 / 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 / actomyosin contractile ring / hypotonic response / uropod / actin-myosin filament sliding / detection of mechanical stimulus / negative regulation of actin filament polymerization / apical cortex / bleb assembly / actomyosin / substrate-dependent cell migration, cell extension / myosin filament / filopodium assembly / early phagosome / myosin II complex / cortical actin cytoskeleton organization / microfilament motor activity / cortical actin cytoskeleton / pseudopodium / cytoskeletal motor activity / cleavage furrow / mitotic cytokinesis / response to mechanical stimulus / 14-3-3 protein binding / response to cAMP / extracellular matrix / cell motility / response to hydrogen peroxide / chemotaxis / actin filament binding / protein localization / regulation of cell shape / cell cortex / 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. / 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: 2.01 Å
AuthorsFrye, J.J. / Klenchin, V.A. / Bagshaw, C.R. / Rayment, I.
CitationJournal: Biochemistry / Year: 2010
Title: Insights into the importance of hydrogen bonding in the gamma-phosphate binding pocket of myosin: structural and functional studies of serine 236
Authors: Frye, J.J. / Klenchin, V.A. / Bagshaw, C.R. / Rayment, I.
History
DepositionMay 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 14, 2011Group: Other
Revision 1.3Sep 6, 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_ref_seq_dif / 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_label_seq_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.ptnr3_label_seq_id / _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_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
X: Myosin-2 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,5905
Polymers86,7311
Non-polymers8594
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.43, 146.44, 153.76
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 X

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


Mass: 86731.109 Da / Num. of mol.: 1 / Mutation: S236A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: DDB_G0286355, mhcA / Plasmid: pDXA / Production host: Dictyostelium discoideum (eukaryote) / Strain (production host): ORF+ / References: UniProt: P08799

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Non-polymers , 5 types, 355 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 2.87 Å3/Da / Density % sol: 57.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 12% PEG8K, 250mM MgCl2, 100mM MOPS, 2mM ADP, 3mM sodium vanadate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 0.97885 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 20, 2005 / Details: 3.3 Undulator
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97885 Å / Relative weight: 1
ReflectionResolution: 2→35.62 Å / Num. all: 64281 / Num. obs: 64281 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 18.6
Reflection shellResolution: 2.01→2.08 Å / Redundancy: 4 % / Rmerge(I) obs: 0.237 / Mean I/σ(I) obs: 2.9 / Num. unique all: 5925 / Rsym value: 0.237 / % possible all: 90.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0066refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1VOM

1vom


Resolution: 2.01→35.62 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.913 / SU B: 3.299 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23958 3262 5.1 %RANDOM
Rwork0.1889 ---
all0.19147 64281 --
obs0.19147 61007 96.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.664 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20 Å20 Å2
2---0.01 Å20 Å2
3----0.54 Å2
Refinement stepCycle: LAST / Resolution: 2.01→35.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5590 0 55 351 5996
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0225816
X-RAY DIFFRACTIONr_angle_refined_deg1.981.9627880
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1745720
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.29224.983287
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.594151012
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.761529
X-RAY DIFFRACTIONr_chiral_restr0.1510.2866
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214430
X-RAY DIFFRACTIONr_mcbond_it1.2041.53542
X-RAY DIFFRACTIONr_mcangle_it2.03225714
X-RAY DIFFRACTIONr_scbond_it3.26732274
X-RAY DIFFRACTIONr_scangle_it4.9594.52158
LS refinement shellResolution: 2.011→2.063 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 200 -
Rwork0.187 4070 -
obs--87.82 %

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