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- PDB-5tr5: Solution structure of Serine 65 phosphorylated UBL domain from parkin -

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Basic information

Entry
Database: PDB / ID: 5tr5
TitleSolution structure of Serine 65 phosphorylated UBL domain from parkin
ComponentsE3 ubiquitin-protein ligase parkin
KeywordsLIGASE / phosphorylation / PINK1 / Parkinson's disease
Function / homology
Function and homology information


positive regulation of retrograde transport, endosome to Golgi / regulation of lipid transport / positive regulation of neurotransmitter uptake / negative regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway / negative regulation of spontaneous neurotransmitter secretion / negative regulation of intralumenal vesicle formation / regulation protein catabolic process at presynapse / cellular response to L-glutamine / : / negative regulation of exosomal secretion ...positive regulation of retrograde transport, endosome to Golgi / regulation of lipid transport / positive regulation of neurotransmitter uptake / negative regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway / negative regulation of spontaneous neurotransmitter secretion / negative regulation of intralumenal vesicle formation / regulation protein catabolic process at presynapse / cellular response to L-glutamine / : / negative regulation of exosomal secretion / mitochondrion to lysosome vesicle-mediated transport / type 2 mitophagy / negative regulation of glucokinase activity / response to curcumin / negative regulation of mitochondrial fusion / cellular response to hydrogen sulfide / protein K29-linked ubiquitination / free ubiquitin chain polymerization / positive regulation of protein linear polyubiquitination / host-mediated suppression of viral genome replication / RBR-type E3 ubiquitin transferase / Parkin-FBXW7-Cul1 ubiquitin ligase complex / regulation of synaptic vesicle transport / positive regulation of mitochondrial fusion / negative regulation of actin filament bundle assembly / positive regulation of mitophagy / F-box domain binding / regulation of necroptotic process / mitochondrial fragmentation involved in apoptotic process / regulation of cellular response to oxidative stress / positive regulation of dendrite extension / regulation of dopamine metabolic process / negative regulation of excitatory postsynaptic potential / norepinephrine metabolic process / autophagy of mitochondrion / dopaminergic synapse / positive regulation of type 2 mitophagy / mitochondrion localization / protein localization to mitochondrion / cellular response to dopamine / mitochondrial fission / positive regulation of protein localization to membrane / positive regulation of proteasomal protein catabolic process / cellular response to toxic substance / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of tumor necrosis factor-mediated signaling pathway / aggresome assembly / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / regulation of mitochondrion organization / cellular response to L-glutamate / protein K11-linked ubiquitination / protein K6-linked ubiquitination / ubiquitin conjugating enzyme binding / regulation of canonical Wnt signaling pathway / negative regulation of synaptic transmission, glutamatergic / positive regulation of mitochondrial membrane potential / negative regulation of JNK cascade / aggresome / protein K27-linked ubiquitination / 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 / Lewy body / startle response / dopamine uptake involved in synaptic transmission / dopamine metabolic process / regulation of dopamine secretion / positive regulation of ATP biosynthetic process / negative regulation of reactive oxygen species metabolic process / regulation of glucose metabolic process / regulation of protein ubiquitination / cellular response to unfolded protein / protein deubiquitination / cullin family protein binding / regulation of synaptic vesicle endocytosis / protein monoubiquitination / negative regulation of mitochondrial fission / ubiquitin ligase complex / protein K63-linked ubiquitination / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / regulation of postsynaptic membrane neurotransmitter receptor levels / protein autoubiquitination / mitophagy / phospholipase binding / negative regulation of reactive oxygen species biosynthetic process / cellular response to manganese ion / ERAD pathway / 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 / Josephin domain DUBs / central nervous system development / regulation of autophagy / PINK1-PRKN Mediated Mitophagy
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 speciesHomo sapiens (human)
MethodSOLUTION NMR / na
AuthorsAguirre, J.D. / Dunkerley, K.M. / Mercier, P. / Shaw, G.S.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-14606 Canada
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structure of phosphorylated UBL domain and insights into PINK1-orchestrated parkin activation.
Authors: Aguirre, J.D. / Dunkerley, K.M. / Mercier, P. / Shaw, G.S.
History
DepositionOct 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2017Group: Database references
Revision 1.2Jan 25, 2017Group: Database references
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Structure summary / Category: entity / pdbx_audit_support
Item: _entity.pdbx_number_of_molecules / _pdbx_audit_support.funding_organization
Revision 1.4Jun 14, 2023Group: Advisory / Database references / Other
Category: database_2 / pdbx_database_remark / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_remark.text / _pdbx_database_status.status_code_nmr_data
Revision 1.5Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI
Remark 650HELIX DETERMINATION METHOD: AUTHOR
Remark 700SHEET DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase parkin


Theoretical massNumber of molelcules
Total (without water)8,9161
Polymers8,9161
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5030 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 50structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein E3 ubiquitin-protein ligase parkin / Parkin / Parkinson juvenile disease protein 2 / Parkinson disease protein 2


Mass: 8916.063 Da / Num. of mol.: 1 / Fragment: residues 1-76
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARK2, PRKN / Plasmid: pET SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O60260, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic12D 1H-15N HSQC
123isotropic12D 1H-13C HSQC aliphatic
135isotropic12D 1H-13C HSQC aromatic
144isotropic13D HNCA
154isotropic13D HN(CA)CB
164isotropic13D HNCO
194isotropic13D C(CO)NH
174isotropic13D (H)CCH-TOCSY
185isotropic12D (HB)CB(CGCD)HD
1113isotropic13D 1H-13C NOESY aliphatic
1125isotropic13D 1H-13C NOESY aromatic
1104isotropic13D 1H-15N NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution2300 uM [U-15N] pUBL, 25 mM HEPES, 100 mM sodium chloride, 250 uM TCEP, 200 uM DSS, 300 uM imidazole, 90% H2O/10% D2O15N90% H2O/10% D2O
solution3300 uM [U-13C] pUBL, 25 mM HEPES, 100 mM sodium chloride, 250 uM TCEP, 200 uM DSS, 300 uM imidazole, 90% H2O/10% D2O13C90% H2O/10% D2O
solution4400 uM [U-99% 13C; U-99% 15N] pUBL, 25 mM HEPES, 100 mM sodium chloride, 250 uM TCEP, 200 uM DSS, 300 uM imidazole, 90% H2O/10% D2O13C/15N90% H2O/10% D2O
solution5400 uM pUBL, 25 mM HEPES, 100 mM sodium chloride, 250 uM TCEP, 200 uM DSS, 300 uM imidazole, 100% D2OD20100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 uMpUBL[U-15N]2
25 mMHEPESnatural abundance2
100 mMsodium chloridenatural abundance2
250 uMTCEPnatural abundance2
200 uMDSSnatural abundance2
300 uMimidazolenatural abundance2
300 uMpUBL[U-13C]3
25 mMHEPESnatural abundance3
100 mMsodium chloridenatural abundance3
250 uMTCEPnatural abundance3
200 uMDSSnatural abundance3
300 uMimidazolenatural abundance3
400 uMpUBL[U-99% 13C; U-99% 15N]4
25 mMHEPESnatural abundance4
100 mMsodium chloridenatural abundance4
250 uMTCEPnatural abundance4
200 uMDSSnatural abundance4
300 uMimidazolenatural abundance4
400 uMpUBLnatural abundance5
25 mMHEPESnatural abundance5
100 mMsodium chloridenatural abundance5
250 uMTCEPnatural abundance5
200 uMDSSnatural abundance5
300 uMimidazolenatural abundance5
Sample conditionsIonic strength: 100 mM / Label: 1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe8.9Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRView8.2.4Johnson, One Moon Scientificdata analysis
VNMR3.2Variancollection
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: na / Software ordinal: 5
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 25

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