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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 / negative regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway / negative regulation of spontaneous neurotransmitter secretion / mitochondrion-derived vesicle / negative regulation of intralumenal vesicle formation / regulation protein catabolic process at presynapse / cellular response to L-glutamine / negative regulation of exosomal secretion / Josephin domain DUBs / mitochondrion to lysosome vesicle-mediated transport ...positive regulation of neurotransmitter uptake / negative regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway / negative regulation of spontaneous neurotransmitter secretion / mitochondrion-derived vesicle / negative regulation of intralumenal vesicle formation / regulation protein catabolic process at presynapse / cellular response to L-glutamine / negative regulation of exosomal secretion / Josephin domain DUBs / mitochondrion to lysosome vesicle-mediated transport / type 2 mitophagy / PINK1-PRKN Mediated Mitophagy / Regulation of necroptotic cell death / response to curcumin / cellular response to hydrogen sulfide / free ubiquitin chain polymerization / negative regulation of mitochondrial fusion / positive regulation of protein linear polyubiquitination / Aggrephagy / RBR-type E3 ubiquitin transferase / host-mediated suppression of viral genome replication / Parkin-FBXW7-Cul1 ubiquitin ligase complex / positive regulation of mitochondrial fusion / negative regulation of actin filament bundle assembly / mitochondrial fragmentation involved in apoptotic process / F-box domain binding / positive regulation of mitophagy / regulation of cellular response to oxidative stress / positive regulation of dendrite extension / regulation of neurotransmitter secretion / regulation of dopamine metabolic process / negative regulation of excitatory postsynaptic potential / norepinephrine metabolic process / autophagy of mitochondrion / positive regulation of type 2 mitophagy / dopaminergic synapse / mitochondrion localization / protein localization to mitochondrion / mitochondrial fission / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / cellular response to toxic substance / positive regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / positive regulation of protein localization to membrane / regulation of mitochondrion organization / Antigen processing: Ubiquitination & Proteasome degradation / protein K11-linked ubiquitination / aggresome assembly / cellular response to L-glutamate / synaptic transmission, dopaminergic / positive regulation of proteasomal protein catabolic process / protein K6-linked ubiquitination / ubiquitin conjugating enzyme binding / aggresome / negative regulation of JNK cascade / negative regulation of synaptic transmission, glutamatergic / positive regulation of mitochondrial membrane potential / regulation of reactive oxygen species metabolic process / positive regulation of mitochondrial fission / response to muscle activity / negative regulation of release of cytochrome c from mitochondria / response to corticosterone / ubiquitin-specific protease binding / intracellular vesicle / startle response / dopamine metabolic process / dopamine uptake involved in synaptic transmission / negative regulation of reactive oxygen species metabolic process / positive regulation of ATP biosynthetic process / regulation of protein ubiquitination / response to unfolded protein / cullin family protein binding / regulation of synaptic vesicle endocytosis / negative regulation of mitochondrial fission / protein monoubiquitination / protein K63-linked ubiquitination / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / ubiquitin ligase complex / regulation of postsynaptic membrane neurotransmitter receptor levels / protein autoubiquitination / mitophagy / negative regulation of reactive oxygen species biosynthetic process / phospholipase binding / cellular response to manganese ion / heat shock protein binding / protein K48-linked ubiquitination / proteasomal protein catabolic process / Hsp70 protein binding / response to endoplasmic reticulum stress / positive regulation of insulin secretion involved in cellular response to glucose stimulus / regulation of autophagy / protein catabolic process / learning / regulation of mitochondrial membrane potential / adult locomotory behavior / PDZ domain binding / ubiquitin binding / mitochondrion organization / regulation of protein stability / synaptic transmission, glutamatergic
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 / 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 / IBR domain / : / 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 domain profile. / Ubiquitin-like domain / 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
Water00
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 / 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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