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- PDB-1jwy: CRYSTAL STRUCTURE OF THE DYNAMIN A GTPASE DOMAIN COMPLEXED WITH G... -

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Basic information

Entry
Database: PDB / ID: 1jwy
TitleCRYSTAL STRUCTURE OF THE DYNAMIN A GTPASE DOMAIN COMPLEXED WITH GDP, DETERMINED AS MYOSIN FUSION
ComponentsMyosin-2 heavy chain,Dynamin-A
KeywordsHYDROLASE / dynamin / GTPase / GDP / 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 / actin-myosin filament sliding / detection of mechanical stimulus / profilin binding / negative regulation of actin filament polymerization / apical cortex / 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 / intercellular bridge / intracellular distribution of mitochondria / pseudopodium / cleavage furrow / cytoskeletal motor activity / mitotic cytokinesis / phagocytosis / response to mechanical stimulus / response to cAMP / phagocytic vesicle / 14-3-3 protein binding / extracellular matrix / actin filament organization / mitochondrion organization / response to bacterium / cell motility / response to hydrogen peroxide / phospholipid binding / chemotaxis / actin filament binding / 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 / GUANOSINE-5'-DIPHOSPHATE / 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 1.4Jul 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_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_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 1.5Aug 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 1.6Nov 20, 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)125,6736
Polymers124,5741
Non-polymers1,0995
Water6,648369
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.550, 61.950, 181.070
Angle α, β, γ (deg.)90.00, 94.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 2 molecules A

#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

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Non-polymers , 4 types, 373 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / 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: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / Source method: isolated from a natural source / Formula: H2O

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Details

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: ESRF / Beamline: ID14-4 / Wavelength: 0.92 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 27, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 50492 / % possible obs: 94 % / Redundancy: 3.4 % / Biso Wilson estimate: 29 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.054 / Net I/σ(I): 15.7
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 4.1 / Rsym value: 0.186 / % possible all: 53.6
Reflection
*PLUS
Lowest resolution: 30 Å / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
% possible obs: 53.6 % / Rmerge(I) obs: 0.186 / Mean I/σ(I) obs: 4.13

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Processing

Software
NameClassification
CNSrefinement
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JX2 (SAME PROTEIN WITHOUT NUCLEOTIDE)

1jx2


Resolution: 2.3→29.4 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.257 3470 6.9 %every-Nth
Rwork0.203 ---
obs0.203 50492 95.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.3413 Å2 / ksol: 0.34314 e/Å3
Displacement parametersBiso mean: 46.6 Å2
Baniso -1Baniso -2Baniso -3
1-5.55 Å20 Å2-1.62 Å2
2--1.2 Å20 Å2
3----6.75 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.3→29.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8297 0 69 369 8735
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_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
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: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.313 392 6.8 %
Rwork0.236 --
obs--64.8 %
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: 6.9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81
LS refinement shell
*PLUS
Rfactor Rfree: 0.313 / % reflection Rfree: 6.8 % / Rfactor Rwork: 0.236

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