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- PDB-1mg8: NMR structure of ubiquitin-like domain in murine Parkin -

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Basic information

Entry
Database: PDB / ID: 1mg8
TitleNMR structure of ubiquitin-like domain in murine Parkin
ComponentsParkin
KeywordsAPOPTOSIS / parkinson disease / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


positive regulation of neurotransmitter uptake / regulation protein catabolic process at presynapse / negative regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway / mitochondrion-derived vesicle / negative regulation of spontaneous neurotransmitter secretion / negative regulation of intralumenal vesicle formation / PINK1-PRKN Mediated Mitophagy / negative regulation of exosomal secretion / Josephin domain DUBs / mitochondrion to lysosome vesicle-mediated transport ...positive regulation of neurotransmitter uptake / regulation protein catabolic process at presynapse / negative regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway / mitochondrion-derived vesicle / negative regulation of spontaneous neurotransmitter secretion / negative regulation of intralumenal vesicle formation / PINK1-PRKN Mediated Mitophagy / negative regulation of exosomal secretion / Josephin domain DUBs / mitochondrion to lysosome vesicle-mediated transport / positive regulation of mitochondrial fusion / Regulation of necroptotic cell death / parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization / cellular response to hydrogen sulfide / Aggrephagy / Parkin-FBXW7-Cul1 ubiquitin ligase complex / negative regulation of mitochondrial fusion / free ubiquitin chain polymerization / negative regulation of actin filament bundle assembly / RBR-type E3 ubiquitin transferase / 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 / dopaminergic synapse / regulation of dopamine metabolic process / regulation of cellular response to oxidative stress / regulation of neurotransmitter secretion / negative regulation of excitatory postsynaptic potential / cellular response to L-glutamate / autophagy of mitochondrion / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / protein K6-linked ubiquitination / Antigen processing: Ubiquitination & Proteasome degradation / 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 / aggresome assembly / ubiquitin conjugating enzyme binding / regulation of mitochondrion organization / aggresome / 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 / 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 / regulation of protein ubiquitination / negative regulation of mitochondrial fission / negative regulation of insulin secretion / negative regulation of reactive oxygen species metabolic process / protein K48-linked ubiquitination / protein autoubiquitination / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / ubiquitin ligase complex / negative regulation of reactive oxygen species biosynthetic process / Hsp70 protein binding / heat shock protein binding / response to endoplasmic reticulum stress / mitochondrion organization / tubulin binding / adult locomotory behavior / regulation of mitochondrial membrane potential / negative regulation of protein phosphorylation / locomotory behavior / ubiquitin binding / synaptic transmission, glutamatergic / learning / regulation of autophagy / G protein-coupled receptor binding / PDZ domain binding / proteasomal protein catabolic process / protein catabolic process
Similarity search - Function
: / : / : / E3 ubiquitin-protein ligase parkin / RING/Ubox-like zinc-binding domain / Parkin, RING/Ubox like zinc-binding domain / RING/Ubox like zinc-binding domain / RING/Ubox like zinc-binding domain / E3 ubiquitin ligase RBR family / IBR domain ...: / : / : / E3 ubiquitin-protein ligase parkin / RING/Ubox-like zinc-binding domain / Parkin, RING/Ubox like zinc-binding domain / RING/Ubox like zinc-binding domain / RING/Ubox like zinc-binding domain / E3 ubiquitin ligase RBR family / IBR domain / In Between Ring fingers / TRIAD supradomain / TRIAD supradomain profile. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase parkin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsTashiro, M. / Okubo, S. / Shimotakahara, S. / Hatanaka, H. / Yasuda, H. / Kainosho, M. / Yokoyama, S. / Shindo, H. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Citation
Journal: J.Biomol.NMR / Year: 2003
Title: NMR structure of ubiquitin-like domain in PARKIN: Gene product of familial Parkinson's disease.
Authors: Tashiro, M. / Okubo, S. / Shimotakahara, S. / Hatanaka, H. / Yasuda, H. / Kainosho, M. / Yokoyama, S. / Shindo, H.
#1: Journal: Nature / Year: 1998
Title: Mutations in the parkin gene causes autosomal recessive juvenile parkinsonism
Authors: Kitada, T. / Asakawa, S. / Hattori, N. / Matsumine, H. / Yamamura, Y. / Minosima, S. / Yokochi, M. / Mizuno, Y. / Shimizu, N.
History
DepositionAug 15, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Dec 21, 2022Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.5May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Parkin


Theoretical massNumber of molelcules
Total (without water)8,9181
Polymers8,9181
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50structures with the lowest energy
Representative

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Components

#1: Protein Parkin


Mass: 8918.294 Da / Num. of mol.: 1 / Fragment: ubiquitin-like domain / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Plasmid: pET28b / Strain: BL21 (DE3) / References: UniProt: Q9WVS6

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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
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: 1mM ubiquitin-like domain U-15N,13C; 25mM acetate buffer NA, 2mM dithiothreitol-d10
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 5.0 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker DRXBrukerDRX6002
Varian INOVAVarianINOVA6003

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Processing

NMR software
NameClassification
X-PLORrefinement
NMRPipeprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10

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