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- PDB-2y0r: Structural basis for the allosteric interference of myosin functi... -

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Basic information

Entry
Database: PDB / ID: 2y0r
TitleStructural basis for the allosteric interference of myosin function by mutants G680A and G680V of Dictyostelium myosin-2
ComponentsMYOSIN-2 HEAVY CHAIN
KeywordsMOTOR PROTEIN
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
Myosin-2 heavy chain
Similarity search - Component
Biological speciesDICTYOSTELIUM DISCOIDEUM (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsPreller, M. / Bauer, S. / Adamek, N. / Fujita-Becker, S. / Fedorov, R. / Geeves, M.A. / Manstein, D.J.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural Basis for the Allosteric Interference of Myosin Function by Reactive Thiol Region Mutations G680A and G680V.
Authors: Preller, M. / Bauer, S. / Adamek, N. / Fujita-Becker, S. / Fedorov, R. / Geeves, M.A. / Manstein, D.J.
History
DepositionDec 7, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2011Group: Database references
Revision 1.2Jun 20, 2018Group: Advisory / Data collection / Derived calculations / Category: pdbx_validate_close_contact / struct_conn
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: MYOSIN-2 HEAVY CHAIN


Theoretical massNumber of molelcules
Total (without water)86,3801
Polymers86,3801
Non-polymers00
Water6,828379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.600, 106.000, 178.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein MYOSIN-2 HEAVY CHAIN / / MYOSIN II HEAVY CHAIN / MYOSIN-2


Mass: 86379.703 Da / Num. of mol.: 1 / Fragment: MOTOR DOMAIN, RESIDUES 2-759 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DICTYOSTELIUM DISCOIDEUM (eukaryote) / Production host: DICTYOSTELIUM DISCOIDEUM (eukaryote) / References: UniProt: P08799
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 379 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN X, GLY 680 TO ALA

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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: 3.1 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growpH: 6.5 / Details: 100 MM MES (PH 6.5), 25% PEG 8000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.9175
DetectorDetector: CCD / Date: Dec 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9175 Å / Relative weight: 1
ReflectionResolution: 2.85→91.29 Å / Num. obs: 23285 / % possible obs: 97.9 % / Observed criterion σ(I): 1.5 / Redundancy: 4.5 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 8.53
Reflection shellResolution: 2.85→2.92 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.61 / % possible all: 77.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MMD

1mmd


Resolution: 2.85→19.98 Å / SU ML: 0.48 / σ(F): 1.35 / Phase error: 30.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3011 1241 5.1 %
Rwork0.2528 --
obs0.2558 24550 98.3 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.904 Å2 / ksol: 0.251 e/Å3
Displacement parametersBiso mean: 35.56 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20 Å20 Å2
2---0.36 Å20 Å2
3---0.96 Å2
Refinement stepCycle: LAST / Resolution: 2.85→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6090 0 0 379 6469
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026208
X-RAY DIFFRACTIONf_angle_d0.5728378
X-RAY DIFFRACTIONf_dihedral_angle_d13.812333
X-RAY DIFFRACTIONf_chiral_restr0.041915
X-RAY DIFFRACTIONf_plane_restr0.0021100
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.96380.38661080.3012183X-RAY DIFFRACTION85
2.9638-3.09820.33711480.29082574X-RAY DIFFRACTION100
3.0982-3.26090.38581360.27782599X-RAY DIFFRACTION100
3.2609-3.46420.35651310.2832620X-RAY DIFFRACTION100
3.4642-3.73010.32921420.24482604X-RAY DIFFRACTION100
3.7301-4.10260.24951340.23142627X-RAY DIFFRACTION100
4.1026-4.68950.26981350.21142633X-RAY DIFFRACTION100
4.6895-5.88310.29911440.24112687X-RAY DIFFRACTION100
5.8831-19.97570.30141630.26312782X-RAY DIFFRACTION100

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