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- PDB-1iyf: Solution structure of ubiquitin-like domain of human parkin -

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Basic information

Entry
Database: PDB / ID: 1iyf
TitleSolution structure of ubiquitin-like domain of human parkin
Componentsparkin
KeywordsLIGASE / Ubiquitin fold / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


positive regulation of retrograde transport, endosome to Golgi / regulation of lipid transport / positive regulation of neurotransmitter uptake / regulation protein catabolic process at presynapse / negative regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway / negative regulation of primary amine oxidase activity / negative regulation of spontaneous neurotransmitter secretion / negative regulation of intralumenal vesicle formation / regulation of protein targeting to mitochondrion / negative regulation of glucokinase activity ...positive regulation of retrograde transport, endosome to Golgi / regulation of lipid transport / positive regulation of neurotransmitter uptake / regulation protein catabolic process at presynapse / negative regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway / negative regulation of primary amine oxidase activity / negative regulation of spontaneous neurotransmitter secretion / negative regulation of intralumenal vesicle formation / regulation of protein targeting to mitochondrion / negative regulation of glucokinase activity / negative regulation of exosomal secretion / mitochondrion to lysosome vesicle-mediated transport / positive regulation of mitochondrial fusion / parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization / protein K29-linked ubiquitination / Lewy body / protein K27-linked ubiquitination / Parkin-FBXW7-Cul1 ubiquitin ligase complex / regulation of synaptic vesicle transport / 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 / positive regulation of mitophagy / cellular response to toxic substance / dopaminergic synapse / regulation of dopamine metabolic process / regulation of necroptotic process / regulation of cellular response to oxidative stress / autophagy of mitochondrion / 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 / protein K11-linked ubiquitination / cellular response to dopamine / positive regulation of tumor necrosis factor-mediated signaling pathway / mitochondrial fission / aggresome assembly / ubiquitin conjugating enzyme binding / regulation of mitochondrion organization / regulation of canonical Wnt signaling pathway / aggresome / ERAD pathway / 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 / regulation of dopamine secretion / ubiquitin-specific protease binding / startle response / negative regulation of release of cytochrome c from mitochondria / protein monoubiquitination / protein K63-linked ubiquitination / cullin family protein binding / phospholipase binding / mitophagy / regulation of protein ubiquitination / regulation of glucose metabolic process / negative regulation of insulin secretion / negative regulation of reactive oxygen species metabolic process / protein K48-linked ubiquitination / cellular response to unfolded protein / positive regulation of DNA binding / cellular response to manganese ion / protein autoubiquitination / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / ubiquitin ligase complex / Hsp70 protein binding / heat shock protein binding / PINK1-PRKN Mediated Mitophagy / response to endoplasmic reticulum stress / mitochondrion organization / tubulin binding / adult locomotory behavior / Josephin domain DUBs / regulation of mitochondrial membrane potential / negative regulation of protein phosphorylation / ubiquitin binding / synaptic transmission, glutamatergic / learning / central nervous system development / regulation of autophagy / G protein-coupled receptor binding / PDZ domain binding / proteasomal protein catabolic process / macroautophagy / protein destabilization / regulation of protein stability / negative regulation of canonical Wnt signaling pathway
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 speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsSakata, E. / Yamaguchi, Y. / Kurimoto, E. / Kikuchi, J. / Yokoyama, S. / Kawahara, H. / Yokosawa, H. / Hattori, N. / Mizuno, Y. / Tanaka, K. ...Sakata, E. / Yamaguchi, Y. / Kurimoto, E. / Kikuchi, J. / Yokoyama, S. / Kawahara, H. / Yokosawa, H. / Hattori, N. / Mizuno, Y. / Tanaka, K. / Kato, K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: EMBO REP. / Year: 2003
Title: Parkin binds the Rpn10 subunit of 26S proteasomes through its ubiquitin-like domain
Authors: Sakata, E. / Yamaguchi, Y. / Kurimoto, E. / Kikuchi, J. / Yokoyama, S. / Yamada, S. / Kawahara, H. / Yokosawa, H. / Hattori, N. / Mizuno, Y. / Tanaka, K. / Kato, K.
History
DepositionAug 13, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / 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 / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: parkin


Theoretical massNumber of molelcules
Total (without water)9,2481
Polymers9,2481
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
RepresentativeModel #1lowest energy

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Components

#1: Protein parkin


Mass: 9247.536 Da / Num. of mol.: 1 / Fragment: ubiquitin-like domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX6P3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Codonplus / References: UniProt: O60260, ubiquitin-protein ligase

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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
2322D 1H-coupled 1H-15N HSQC
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.1mM parkin ubiquitin-like domain U-15N, 13C; 50mM potassium phosphate buffer90% H2O/10% D2O
20.1mM parkin ubiquitin-like domain U-15N, 13C; 50mM potassium phosphate buffer90% H2O, 10% D2O, 5%-DMPC/DHPC; 90% H2O, 10% D2O, 5%-DMPC/DHPC/CTAB
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.3 6.0 1 atm303 K
20.3 6.0 1 atm310 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 spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6collection
XwinNMR2.6data analysis
XwinNMR2.6processing
CNS1.1Brungerstructure solution
CNS1.1Brungerrefinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 720 restraints, 489 are NOE-derived distance constraints, 82 dihedral angle restraints, 129 residual dipolar coupling constraints, 20 distance ...Details: The structures are based on a total of 720 restraints, 489 are NOE-derived distance constraints, 82 dihedral angle restraints, 129 residual dipolar coupling constraints, 20 distance restraints for hydrogen bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10

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