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- PDB-2aka: Structure of the nucleotide-free myosin II motor domain from Dict... -

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Basic information

Entry
Database: PDB / ID: 2aka
TitleStructure of the nucleotide-free myosin II motor domain from Dictyostelium discoideum fused to the GTPase domain of dynamin 1 from Rattus norvegicus
Components
  • Dynamin-1
  • LINKER
  • myosin II heavy chain
KeywordsCONTRACTILE PROTEIN / fusion protein / GTPase domain / dynamin / myosin
Function / homology
Function and homology information


positive regulation of synaptic vesicle recycling / Toll Like Receptor 4 (TLR4) Cascade / clathrin coat assembly involved in endocytosis / vesicle scission / presynaptic endocytic zone membrane / calcium-dependent ATPase activity / pseudopodium retraction / uropod retraction / varicosity / cytoplasmic actin-based contraction involved in forward cell motility ...positive regulation of synaptic vesicle recycling / Toll Like Receptor 4 (TLR4) Cascade / clathrin coat assembly involved in endocytosis / vesicle scission / presynaptic endocytic zone membrane / calcium-dependent ATPase activity / pseudopodium retraction / uropod retraction / varicosity / cytoplasmic actin-based contraction involved in forward cell motility / phagocytic cup base / pathogen-containing vacuole / response to differentiation-inducing factor 1 / equatorial cell cortex / synaptic vesicle budding from presynaptic endocytic zone membrane / contractile actin filament bundle assembly / cell trailing edge / contractile vacuole organization / myosin filament assembly / Gap junction degradation / Formation of annular gap junctions / aggregation involved in sorocarp development / culmination involved in sorocarp development / RHO GTPases activate PAKs / adenyl nucleotide binding / hypotonic response / actomyosin contractile ring / dynamin GTPase / uropod / MHC class II antigen presentation / chromaffin granule / regulation of vesicle size / photoreceptor ribbon synapse / Recycling pathway of L1 / apical cortex / detection of mechanical stimulus / negative regulation of actin filament polymerization / actin-myosin filament sliding / positive regulation of synaptic vesicle endocytosis / endosome organization / Clathrin-mediated endocytosis / bleb assembly / actomyosin / substrate-dependent cell migration, cell extension / membrane coat / filopodium assembly / myosin filament / early phagosome / G protein-coupled receptor internalization / myosin II complex / clathrin-coated vesicle / cortical actin cytoskeleton organization / nitric-oxide synthase binding / cortical actin cytoskeleton / microfilament motor activity / pseudopodium / regulation of synaptic vesicle endocytosis / phosphatidylinositol-3,4,5-trisphosphate binding / response to amyloid-beta / cytoskeletal motor activity / cleavage furrow / mitotic cytokinesis / synaptic vesicle endocytosis / endocytic vesicle / response to mechanical stimulus / response to cAMP / D2 dopamine receptor binding / clathrin-coated pit / protein serine/threonine kinase binding / 14-3-3 protein binding / phosphatidylinositol-4,5-bisphosphate binding / photoreceptor inner segment / extracellular matrix / receptor-mediated endocytosis / cell motility / modulation of chemical synaptic transmission / protein homooligomerization / response to hydrogen peroxide / receptor internalization / SH3 domain binding / endocytosis / chemotaxis / actin filament binding / GDP binding / intracellular protein localization / synaptic vesicle / regulation of cell shape / presynapse / cell cortex / microtubule binding / cytoplasmic vesicle / protein homotetramerization / microtubule / cytoskeleton / calmodulin binding / GTPase activity / synapse / protein-containing complex binding / protein kinase binding / GTP binding
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #60 / Dynamin GTPase effector / Dynamin GTPase effector domain / Dynamin GTPase effector domain / Dynamin, GTPase region, conserved site / Dynamin-type guanine nucleotide-binding (G) domain signature. / Dynamin stalk domain / Dynamin central region / GTPase effector domain / GED domain profile. ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #60 / Dynamin GTPase effector / Dynamin GTPase effector domain / Dynamin GTPase effector domain / Dynamin, GTPase region, conserved site / Dynamin-type guanine nucleotide-binding (G) domain signature. / Dynamin stalk domain / Dynamin central region / GTPase effector domain / GED domain profile. / Dynamin, GTPase domain / Dynamin, GTPase / Dynamin / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #530 / Dynamin-type guanine nucleotide-binding (G) domain / Dynamin-type guanine nucleotide-binding (G) domain profile. / Dynamin, N-terminal / Dynamin family / 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. / PH domain / Kinesin motor domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / PH-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Myosin-2 heavy chain / Dynamin-1
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.9 Å
AuthorsReubold, T.F. / Eschenburg, S. / Becker, A. / Leonard, M. / Schmid, S.L. / Vallee, R.B. / Kull, F.J. / Manstein, D.J.
Citation
#1: Journal: Nat.Struct.Mol.Biol. / Year: 2003
Title: A structural model for actin-induced nucleotide release in myosin
Authors: Reubold, T.F. / Eschenburg, S. / Becker, A. / Kull, F.J. / Manstein, D.J.
History
DepositionAug 3, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: myosin II heavy chain
L: LINKER
B: Dynamin-1


Theoretical massNumber of molelcules
Total (without water)123,2543
Polymers123,2543
Non-polymers00
Water13,583754
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.420, 126.990, 160.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein myosin II heavy chain


Mass: 88594.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: fused to a linker and dynamin-1 / Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: MHCA / Production host: Dictyostelium discoideum (eukaryote) / Strain (production host): AX3-ORF+ / References: UniProt: P08799
#2: Protein/peptide LINKER


Mass: 1442.661 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHETIC LINKER
#3: Protein Dynamin-1 / D100 / Dynamin / brain / B-dynamin


Mass: 33217.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: fused to myosin and linker / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Dnm1, Dnm / Production host: Dictyostelium discoideum (eukaryote) / Strain (production host): AX3-ORF+ / References: UniProt: P21575, dynamin GTPase
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 754 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Tris, PEG 8000, MPD, DTT, magnesium chloride, pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93927 / Wavelength: 0.93927 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 14, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93927 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 92665 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 19.3 Å2 / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 18.1
Reflection shellResolution: 1.9→2 Å / % possible all: 94.9

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Processing

Software
NameClassification
CAD4data collection
XDSdata reduction
CNSrefinement
CAD4data reduction
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.9→19.93 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.224 2317 2.5 %RANDOM
Rwork0.185 ---
obs0.185 92658 99.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.91 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 31.6 Å2
Baniso -1Baniso -2Baniso -3
1-8.8 Å20 Å20 Å2
2---6.71 Å20 Å2
3----2.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8623 0 0 754 9377
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_improper_angle_d1.13
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.248 367 2.5 %
Rwork0.194 14287 -
obs--95.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CIS_PEPTIDE.PARAM

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