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- PDB-2jmo: IBR domain of Human Parkin -

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Basic information

Entry
Database: PDB / ID: 2jmo
TitleIBR domain of Human Parkin
ComponentsParkin
KeywordsLIGASE / Parkin / IBR / E3 ligase / zinc binding domain / RBR
Function / homology
Function and homology information


negative regulation of primary amine oxidase 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 spontaneous neurotransmitter secretion / regulation of protein targeting to mitochondrion / negative regulation of intralumenal vesicle formation / negative regulation of glucokinase activity ...negative regulation of primary amine oxidase 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 spontaneous neurotransmitter secretion / regulation of protein targeting to mitochondrion / negative regulation of intralumenal vesicle formation / 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 / positive regulation of mitophagy in response to mitochondrial depolarization / RBR-type E3 ubiquitin transferase / 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 / regulation of dopamine metabolic process / regulation of necroptotic process / dopaminergic synapse / 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 / negative regulation of JNK cascade / positive regulation of protein localization to membrane / 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 canonical Wnt signaling pathway / regulation of mitochondrion organization / aggresome / 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 / ERAD pathway / negative regulation of release of cytochrome c from mitochondria / protein monoubiquitination / protein K63-linked ubiquitination / phospholipase binding / cullin family protein binding / mitophagy / regulation of protein ubiquitination / regulation of glucose metabolic process / negative regulation of insulin secretion / negative regulation of reactive oxygen species metabolic process / cellular response to unfolded protein / positive regulation of DNA binding / cellular response to manganese ion / protein autoubiquitination / protein K48-linked ubiquitination / 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 / proteasomal protein catabolic process / Josephin domain DUBs / negative regulation of protein phosphorylation / regulation of mitochondrial membrane potential / ubiquitin binding / learning / central nervous system development / synaptic transmission, glutamatergic / regulation of autophagy / G protein-coupled receptor binding / PDZ domain binding / macroautophagy / protein destabilization / regulation of protein stability / negative regulation of canonical Wnt signaling pathway
Similarity search - Function
N-terminal domain of TfIIb - #20 / : / : / : / 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 ...N-terminal domain of TfIIb - #20 / : / : / : / 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. / N-terminal domain of TfIIb / Single Sheet / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase parkin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
AuthorsBeasley, S.A. / Hristova, V.A. / Shaw, G.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2007
Title: Structure of the Parkin in-between-ring domain provides insights for E3-ligase dysfunction in autosomal recessive Parkinson's disease.
Authors: Beasley, S.A. / Hristova, V.A. / Shaw, G.S.
History
DepositionNov 24, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site
Remark 700SHEET THE AUTHORS STATE THAT CD, NOE AND CHEMICAL SHIFT INDEX DATA ARE NOT CONSISTENT WITH BETA ...SHEET THE AUTHORS STATE THAT CD, NOE AND CHEMICAL SHIFT INDEX DATA ARE NOT CONSISTENT WITH BETA SHEET CHARACTER IN THIS PROTEIN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Parkin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7493
Polymers8,6191
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Parkin / Ubiquitin E3 ligase PRKN / Parkinson juvenile disease protein 2 / Parkinson disease protein 2


Mass: 8618.604 Da / Num. of mol.: 1 / Fragment: IBR-type 1 domain, residues 308-384
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARK2, PRKN
Plasmid details: the thrombin site of pET15b has been replaced with a TEV recognition site
Plasmid: p11 (modified pET15b) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) STAR
References: UniProt: O60260, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1212D 1H-13C HSQC
1323D HNCO
1423D HNCA
1523D HN(CA)CB
1623D CBCA(CO)NH
1723D H(CCO)NH
1823D C(CO)NH
1913D (H)CCH-TOCSY
11013D HBCBCHCDHD
11112D NOESY
11223D 1H-15N NOESY
11313D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.2 mM [U-100% 13C, U-100% 15N] IBR, 25 mM sodium phosphate, 100 mM sodium chloride, 1 mM DTT, 0.033 mM DSS, 100% D2O100% D2O
20.2 mM [U-100% 13C, U-100% 15N] IBR, 25 mM sodium phosphate, 100 mM sodium chloride, 1 mM DTT, 0.033 mM DSS, 90% H2O, 10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.2 mMIBR[U-100% 13C; U-100% 15N]1
25 mMsodium phosphate1
100 mMsodium chloride1
1 mMDTT1
0.033 mMDSS1
0.2 mMIBR[U-100% 13C; U-100% 15N]2
25 mMsodium phosphate2
100 mMsodium chloride2
1 mMDTT2
0.033 mMDSS2
Sample conditionsIonic strength: 100 mM NaCl, 25 mM Na2HPO4 / pH: 6.95 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1bVarianstructure solution
NMRView5.0.4.sol7Johnson, One Moon Scientificdata analysis
NMRView5.0.4.sol7Johnson, One Moon Scientificprocessing
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANA2.5.4Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
Details: The authors state that they used a CYANA residue library with a modified Cysteine - zinc ligand for use in the structure calculations. These were the angles and lengths listed.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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