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- PDB-1jx2: CRYSTAL STRUCTURE OF THE NUCLEOTIDE-FREE DYNAMIN A GTPASE DOMAIN,... -

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Basic information

Entry
Database: PDB / ID: 1jx2
TitleCRYSTAL STRUCTURE OF THE NUCLEOTIDE-FREE DYNAMIN A GTPASE DOMAIN, DETERMINED AS MYOSIN FUSION
ComponentsMyosin-2 heavy chain,Dynamin-A
KeywordsHYDROLASE / dynamin / GTPase / myosin / fusion-protein / Dictyostelium
Function / homology
Function and homology information


protein processing in phagocytic vesicle / Regulation of Apoptosis / Apoptotic execution phase / sorocarp morphogenesis / regulation of post-lysosomal vacuole size / ISG15 antiviral mechanism / phagosome acidification / protein localization to cleavage furrow / pinocytosis / calcium-dependent ATPase activity ...protein processing in phagocytic vesicle / Regulation of Apoptosis / Apoptotic execution phase / sorocarp morphogenesis / regulation of post-lysosomal vacuole size / ISG15 antiviral mechanism / phagosome acidification / protein localization to cleavage furrow / pinocytosis / 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 / hypotonic response / actomyosin contractile ring / uropod / peroxisome fission / profilin binding / apical cortex / detection of mechanical stimulus / negative regulation of actin filament polymerization / actin-myosin filament sliding / endosome organization / bleb assembly / actomyosin / substrate-dependent cell migration, cell extension / midbody abscission / filopodium assembly / myosin filament / early phagosome / mitochondrial fission / myosin II complex / cortical actin cytoskeleton organization / cortical actin cytoskeleton / microfilament motor activity / establishment or maintenance of cell polarity / nucleus organization / intracellular distribution of mitochondria / pseudopodium / cytoskeletal motor activity / cleavage furrow / mitotic cytokinesis / phagocytosis / intercellular bridge / response to mechanical stimulus / response to cAMP / phagocytic vesicle / 14-3-3 protein binding / extracellular matrix / actin filament organization / mitochondrion organization / cell motility / response to bacterium / response to hydrogen peroxide / phospholipid binding / chemotaxis / actin filament binding / intracellular protein localization / regulation of cell shape / cell cortex / microtubule binding / cytoplasmic vesicle / microtubule / cytoskeleton / calmodulin binding / GTPase activity / GTP binding / ATP binding / identical protein binding / membrane / cytosol / cytoplasm
Similarity search - Function
Myosin S1 fragment, N-terminal / 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. ...Myosin S1 fragment, N-terminal / 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 / Kinesin motor domain / Kinesin / 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / SH3 type barrels. / Roll / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / beta-D-glucopyranose / Myosin-2 heavy chain / Dynamin-A
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsNiemann, H.H. / Knetsch, M.L.W. / Scherer, A. / Manstein, D.J. / Kull, F.J.
CitationJournal: EMBO J. / Year: 2001
Title: Crystal structure of a dynamin GTPase domain in both nucleotide-free and GDP-bound forms.
Authors: Niemann, H.H. / Knetsch, M.L. / Scherer, A. / Manstein, D.J. / Kull, F.J.
History
DepositionSep 5, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 31, 2017Group: Structure summary
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.7Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details
Remark 999SEQUENCE According to the author, Electron density map confirm residue 260 to be SER and residue ...SEQUENCE According to the author, Electron density map confirm residue 260 to be SER and residue 323 to be CYS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)125,2054
Polymers124,5741
Non-polymers6323
Water6,774376
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.450, 62.040, 181.200
Angle α, β, γ (deg.)90.00, 94.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Myosin-2 heavy chain,Dynamin-A / Myosin II heavy chain


Mass: 124573.531 Da / Num. of mol.: 1 / Fragment: catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: mhcA, DDB_G0286355, dymA, DDB_G0277849 / Plasmid: pM3 / Production host: Dictyostelium discoideum (eukaryote) / Strain (production host): AX3-Orf+ / References: UniProt: P08799, UniProt: Q94464
#2: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#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.: 376 / 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: 2.468 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 8000, Tris, potassium chloride, magnesium chloride, glucose, methyl-propane-diol, dithiothreitol, EGTA, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
111 %PEG80001reservoir
250 mMTris1reservoir
3200 mM1reservoirKCl
45 mM1reservoirMgCl2
510 %glucose1reservoir
62 %MPD1reservoir
71 mMEGTA1reservoir
85 mMdithiothreitol1reservoir
950 mMTris1drop
101 mM1dropMgCl2
111 mMdithiothreitol1drop
123 %sucrose1drop
135 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Oct 13, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→15 Å / Num. obs: 52742 / % possible obs: 97.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.05 / Net I/σ(I): 19.3
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 3 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 4.98 / Rsym value: 0.215 / % possible all: 94.6
Reflection
*PLUS
Lowest resolution: 15 Å / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 94.6 % / Rmerge(I) obs: 0.215

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Processing

Software
NameClassification
CNSrefinement
MAR345data collection
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G8X, MYOSIN II CATALYTIC DOMAIN

1g8x


Resolution: 2.3→14.96 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 380278.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.255 3692 7 %EVERY-NTH
Rwork0.197 ---
obs0.197 52742 98.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.3914 Å2 / ksol: 0.366682 e/Å3
Displacement parametersBiso mean: 38.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20 Å2-0.24 Å2
2---1.61 Å20 Å2
3---0.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.3→14.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8297 0 40 376 8713
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.298 593 7 %
Rwork0.223 7879 -
obs--95.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER_REP.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 7 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 38.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78
LS refinement shell
*PLUS
Rfactor Rfree: 0.298 / % reflection Rfree: 7 % / Rfactor Rwork: 0.223

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