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- PDB-3mkd: Crystal structure of myosin-2 dictyostelium discoideum motor doma... -

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Basic information

Entry
Database: PDB / ID: 3mkd
TitleCrystal structure of myosin-2 dictyostelium discoideum motor domain S456Y mutant in complex with adp-orthovanadate
ComponentsMyosin-2 heavy chain
KeywordsCONTRACTILE PROTEIN / ALLOSTERIC / METHYLATION / ATP-BINDING / MOTOR PROTEIN / ACTIN-BINDING / PHOSPHOPROTEIN / ADP-ORTHOVANADATE / CALMODULIN-BINDING / NUCLEOTIDE-BINDING / MYOSIN
Function / homology
Function and homology information


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 / pseudopodium retraction / cell trailing edge ...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 / pseudopodium retraction / cell trailing edge / contractile vacuole organization / myosin filament assembly / aggregation involved in sorocarp development / culmination involved in sorocarp development / adenyl nucleotide binding / calcium-dependent ATPase activity / actomyosin contractile ring / hypotonic response / uropod / filopodium assembly / negative regulation of actin filament polymerization / apical cortex / bleb assembly / actin-myosin filament sliding / detection of mechanical stimulus / substrate-dependent cell migration, cell extension / actomyosin / early phagosome / myosin filament / cortical actin cytoskeleton organization / myosin II complex / cortical actin cytoskeleton / microfilament motor activity / cleavage furrow / pseudopodium / mitotic cytokinesis / cytoskeletal motor activity / response to mechanical stimulus / response to cAMP / 14-3-3 protein binding / cell motility / response to hydrogen peroxide / intracellular protein localization / chemotaxis / regulation of cell shape / actin filament binding / cytoplasmic vesicle / extracellular matrix / cell cortex / cytoskeleton / calmodulin binding / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Myosin S1 fragment, N-terminal / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #530 / 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 motor domain profile. / Myosin head, motor domain ...Myosin S1 fragment, N-terminal / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #530 / 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 motor domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin. Large ATPases. / IQ motif profile. / Kinesin motor domain superfamily / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / SH3 type barrels. / Roll / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / VANADATE ION / Myosin-2 heavy chain
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKathmann, D. / Diensthuber, R.P. / Fedorov, R. / Manstein, D.J. / Tsiavaliaris, G.
CitationJournal: To be Published
Title: Switch-2 dependent modulation of the myosin power stroke
Authors: Kathmann, D. / Diensthuber, R.P. / Fedorov, R. / Manstein, D.J. / Tsiavaliaris, G.
History
DepositionApr 14, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_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.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
Revision 2.0Aug 12, 2026Group: Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / pdbx_entry_details ...chem_comp / pdbx_entry_details / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order
Item: _chem_comp.formula / Description: Metalloprotein remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myosin-2 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2584
Polymers78,6921
Non-polymers5663
Water5,837324
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.601, 147.356, 153.899
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-1130-

HOH

21A-1180-

HOH

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Components

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


Mass: 78691.961 Da / Num. of mol.: 1 / Fragment: Myosin-2 motor domain, UNP residues 2-693 / Mutation: S456Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Plasmid: pDXA-3h / Production host: Dictyostelium discoideum (eukaryote) / Strain (production host): ORF+ / References: UniProt: P08799, EC: 3.6.4.1
#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: O4V
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 3.23 Å3/Da / Density % sol: 61.89 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 50mM HEPES, 140mM sodium chloride, 11%(w/v) PEG 5000, 5mM magnesium chloride, 5mM DTT, 1mM EGTA, 2%(v/v) MPD, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 278K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID23-111.00905
SYNCHROTRONBESSY 14.121.00605
Detector
TypeIDDetectorDateDetails (eV)
ADSC QUANTUM 315r1CCDMay 12, 2008bent cylindrical mirror
ADSC QUANTUM 2102CCDJan 27, 2010mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Single Silicon (111) monochromatorSINGLE WAVELENGTHMx-ray1
2Double Crystal MonochromatorSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.009051
21.006051
ReflectionResolution: 2.2→15 Å / Num. all: 49256 / Num. obs: 49256 / % possible obs: 94.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Redundancy: 5.3 % / Biso Wilson estimate: 43.12 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.069 / Net I/σ(I): 16.2
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 2.9 / Num. unique all: 4468 / Rsym value: 0.47 / % possible all: 70.1

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Processing

Software
NameVersionClassification
MxCuBEdata collection
AMoREphasing
CNS1.1refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VOM

1vom


Resolution: 2.4→8 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2399 1940 -RANDOM
Rwork0.1985 ---
all0.2 38972 --
obs0.2 38972 100 %-
Solvent computationBsol: 97.578 Å2
Displacement parametersBiso mean: 41.584 Å2
Baniso -1Baniso -2Baniso -3
1--8.577 Å20 Å20 Å2
2---0.529 Å20 Å2
3---9.107 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5545 0 33 324 5902
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0087
X-RAY DIFFRACTIONc_angle_d1.37
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3vo4.param
X-RAY DIFFRACTION4ADP.param
X-RAY DIFFRACTION5water_rep.param

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