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- PDB-2ys1: Solution structure of the PH domain of Dynamin-2 from human -

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Basic information

Entry
Database: PDB / ID: 2ys1
TitleSolution structure of the PH domain of Dynamin-2 from human
ComponentsDynamin-2
KeywordsSIGNALING PROTEIN / PH domain / dynamin 2 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


organelle fission / cellular response to carbon monoxide / postsynaptic endocytic zone membrane / : / negative regulation of non-motile cilium assembly / negative regulation of membrane tubulation / regulation of Golgi organization / positive regulation of clathrin-dependent endocytosis / positive regulation of P-type sodium:potassium-exchanging transporter activity / synaptic vesicle budding from presynaptic endocytic zone membrane ...organelle fission / cellular response to carbon monoxide / postsynaptic endocytic zone membrane / : / negative regulation of non-motile cilium assembly / negative regulation of membrane tubulation / regulation of Golgi organization / positive regulation of clathrin-dependent endocytosis / positive regulation of P-type sodium:potassium-exchanging transporter activity / synaptic vesicle budding from presynaptic endocytic zone membrane / macropinocytosis / NOSTRIN mediated eNOS trafficking / transferrin transport / dynamin GTPase / regulation of nitric-oxide synthase activity / postsynaptic neurotransmitter receptor internalization / WW domain binding / regulation of Rac protein signal transduction / Toll Like Receptor 4 (TLR4) Cascade / Retrograde neurotrophin signalling / Formation of annular gap junctions / cellular response to X-ray / clathrin-coated endocytic vesicle / Gap junction degradation / Golgi to plasma membrane transport / membrane organization / phosphatidylinositol 3-kinase regulatory subunit binding / coronary vasculature development / NGF-stimulated transcription / cellular response to dopamine / mitochondrial fission / G protein-coupled receptor internalization / regulation of synapse structure or activity / aorta development / ventricular septum development / regulation of axon extension / Lysosome Vesicle Biogenesis / synaptic vesicle transport / Golgi Associated Vesicle Biogenesis / dendritic spine head / nitric-oxide synthase binding / Recycling pathway of L1 / phagocytic cup / response to light stimulus / cellular response to nitric oxide / postsynaptic density, intracellular component / D2 dopamine receptor binding / phagocytosis / positive regulation of lamellipodium assembly / clathrin-coated pit / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of phagocytosis / MHC class II antigen presentation / photoreceptor inner segment / neuron projection morphogenesis / receptor-mediated endocytosis / response to cocaine / mitochondrial membrane / negative regulation of transforming growth factor beta receptor signaling pathway / trans-Golgi network / receptor internalization / ruffle membrane / SH3 domain binding / endocytosis / phagocytic vesicle membrane / G2/M transition of mitotic cell cycle / antigen processing and presentation of exogenous peptide antigen via MHC class II / endocytic vesicle membrane / microtubule cytoskeleton / positive regulation of nitric oxide biosynthetic process / presynapse / lamellipodium / Clathrin-mediated endocytosis / midbody / growth cone / cytoplasmic vesicle / spermatogenesis / microtubule binding / postsynaptic membrane / microtubule / dendritic spine / membrane fusion / postsynaptic density / endosome / positive regulation of apoptotic process / axon / Golgi membrane / focal adhesion / GTPase activity / centrosome / glutamatergic synapse / synapse / protein-containing complex binding / regulation of DNA-templated transcription / GTP binding / protein kinase binding / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / Golgi apparatus / enzyme binding
Similarity search - Function
Dynamin-2 / 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-2 / 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 / Dynamin-type guanine nucleotide-binding (G) domain / Dynamin-type guanine nucleotide-binding (G) domain profile. / Dynamin family / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Roll / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsLi, H. / Sato, M. / Tochio, N. / Koshiba, S. / Watanabe, S. / Harada, T. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the PH domain of Dynamin-2 from human
Authors: Li, H. / Sato, M. / Tochio, N. / Koshiba, S. / Watanabe, S. / Harada, T. / Kigawa, T. / Yokoyama, S.
History
DepositionApr 3, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dynamin-2


Theoretical massNumber of molelcules
Total (without water)13,0781
Polymers13,0781
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Dynamin-2


Mass: 13077.794 Da / Num. of mol.: 1 / Fragment: PH domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: cell-free protein synthesis / Gene: DNM2 / Plasmid: P060904-04 / References: UniProt: P50570

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY

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Sample preparation

DetailsContents: 1.17mM PH domain U-15N,13C; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 296 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
NMRPipe20031121Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.982Kobayashi, N.data analysis
CYANA2.0.17Guntert, P.structure solution
CYANA2.0.17Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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