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Yorodumi- PDB-2knb: Solution NMR structure of the parkin Ubl domain in complex with t... -
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-Basic information
Entry | Database: PDB / ID: 2knb | ||||||
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Title | Solution NMR structure of the parkin Ubl domain in complex with the endophilin-A1 SH3 domain | ||||||
Components |
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Keywords | PROTEIN BINDING / Ubl / SH3 / parkin / endophilin / Cell junction / Cell membrane / Cell projection / Endoplasmic reticulum / Ligase / Membrane / Metal-binding / Nucleus / Postsynaptic cell membrane / S-nitrosylation / Synapse / Ubl conjugation pathway / Zinc-finger / Endocytosis / Lipid-binding / Phosphoprotein / SH3 domain | ||||||
Function / homology | Function and homology information Josephin domain DUBs / Negative regulation of MET activity / membrane bending / Aggrephagy / positive regulation of membrane tubulation / EGFR downregulation / lipid tube assembly / positive regulation of neurotransmitter uptake / regulation protein catabolic process at presynapse / negative regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway ...Josephin domain DUBs / Negative regulation of MET activity / membrane bending / Aggrephagy / positive regulation of membrane tubulation / EGFR downregulation / lipid tube assembly / positive regulation of neurotransmitter uptake / regulation protein catabolic process at presynapse / negative regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway / cellular response to L-glutamine / PINK1-PRKN Mediated Mitophagy / negative regulation of spontaneous neurotransmitter secretion / negative regulation of intralumenal vesicle formation / Antigen processing: Ubiquitination & Proteasome degradation / membrane tubulation / vesicle scission / negative regulation of glucokinase activity / negative regulation of exosomal secretion / mitochondrion to lysosome vesicle-mediated transport / basal dendrite / regulation of clathrin-dependent endocytosis / response to curcumin / positive regulation of mitochondrial fusion / parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization / Retrograde neurotrophin signalling / cellular response to hydrogen sulfide / Lysosome Vesicle Biogenesis / regulation of receptor internalization / negative regulation of blood-brain barrier permeability / synaptic vesicle uncoating / Parkin-FBXW7-Cul1 ubiquitin ligase complex / negative regulation of mitochondrial fusion / free ubiquitin chain polymerization / negative regulation of actin filament bundle assembly / Golgi Associated Vesicle Biogenesis / dendrite extension / RBR-type E3 ubiquitin transferase / MHC class II antigen presentation / positive regulation of mitophagy in response to mitochondrial depolarization / positive regulation of protein linear polyubiquitination / F-box domain binding / negative regulation by host of viral genome replication / mitochondrion localization / positive regulation of autophagy of mitochondrion / positive regulation of mitophagy / mitochondrial fragmentation involved in apoptotic process / cellular response to toxic substance / postsynaptic actin cytoskeleton organization / dopaminergic synapse / Recycling pathway of L1 / regulation of dopamine metabolic process / regulation of cellular response to oxidative stress / regulation of neurotransmitter secretion / negative regulation of excitatory postsynaptic potential / photoreceptor ribbon synapse / cellular response to L-glutamate / autophagy of mitochondrion / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / protein K6-linked ubiquitination / positive regulation of dendrite extension / norepinephrine metabolic process / positive regulation of proteasomal protein catabolic process / protein localization to mitochondrion / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / positive regulation of protein localization to membrane / negative regulation of JNK cascade / negative regulation of synaptic transmission, glutamatergic / protein K11-linked ubiquitination / protein metabolic process / synaptic transmission, dopaminergic / positive regulation of tumor necrosis factor-mediated signaling pathway / mitochondrial fission / presynaptic cytosol / aggresome assembly / ubiquitin conjugating enzyme binding / regulation of mitochondrion organization / aggresome / response to muscle activity / positive regulation of mitochondrial membrane potential / regulation of reactive oxygen species metabolic process / regulation of synaptic vesicle endocytosis / dopamine uptake involved in synaptic transmission / positive regulation of mitochondrial fission / dopamine metabolic process / intracellular vesicle / response to corticosterone / ubiquitin-specific protease binding / positive regulation of ATP biosynthetic process / startle response / negative regulation of release of cytochrome c from mitochondria / protein monoubiquitination / regulation of postsynaptic membrane neurotransmitter receptor levels / protein K63-linked ubiquitination / cullin family protein binding / positive regulation of insulin secretion involved in cellular response to glucose stimulus / phospholipase binding / mitophagy Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Trempe, J. / Guennadi, K. / Edna, C.M. / Kalle, G. | ||||||
Citation | Journal: Mol.Cell / Year: 2009 Title: SH3 domains from a subset of BAR proteins define a Ubl-binding domain and implicate parkin in synaptic ubiquitination. Authors: Trempe, J.F. / Chen, C.X. / Grenier, K. / Camacho, E.M. / Kozlov, G. / McPherson, P.S. / Gehring, K. / Fon, E.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2knb.cif.gz | 926.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2knb.ent.gz | 789.2 KB | Display | PDB format |
PDBx/mmJSON format | 2knb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kn/2knb ftp://data.pdbj.org/pub/pdb/validation_reports/kn/2knb | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 9149.449 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Park2, Prkn / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / Variant (production host): BL21 DE3 References: UniProt: Q9JK66, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) |
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#2: Protein | Mass: 7981.790 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Sh3gl2, Sh3d2a, Sh3p4 / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / Variant (production host): BL21 DE3 / References: UniProt: O35179 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 50 / pH: 7.0 / Pressure: ambient / Temperature: 303 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: HADDOCK used to dock Ubl and SH3 crystal structures using intermolecular NOEs and RDCs | ||||||||||||||||||||||||
NMR constraints | NOE constraints total: 64 / NOE intraresidue total count: 6 / NOE long range total count: 36 / NOE medium range total count: 2 / NOE sequential total count: 20 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 1 / Protein phi angle constraints total count: 71 / Protein psi angle constraints total count: 71 | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 5 ° / Maximum upper distance constraint violation: 0.5 Å | ||||||||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0.02 Å |