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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


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 / RBR-type E3 ubiquitin transferase / host-mediated suppression of viral genome replication / regulation of synaptic vesicle transport / Parkin-FBXW7-Cul1 ubiquitin ligase complex / positive regulation of mitochondrial fusion / negative regulation of actin filament bundle assembly / positive regulation of mitophagy / regulation of necroptotic process / mitochondrial fragmentation involved in apoptotic process / F-box domain binding / 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 / positive regulation of type 2 mitophagy / dopaminergic synapse / mitochondrion localization / protein localization to mitochondrion / cellular response to dopamine / mitochondrial fission / positive regulation of protein localization to membrane / 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 / regulation of mitochondrion organization / protein K11-linked ubiquitination / aggresome assembly / cellular response to L-glutamate / positive regulation of proteasomal protein catabolic process / protein K6-linked ubiquitination / ubiquitin conjugating enzyme binding / regulation of canonical Wnt signaling pathway / aggresome / negative regulation of synaptic transmission, glutamatergic / negative regulation of JNK cascade / protein K27-linked ubiquitination / 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 / Lewy body / ubiquitin-specific protease binding / startle response / dopamine metabolic process / dopamine uptake involved in synaptic transmission / regulation of dopamine secretion / negative regulation of reactive oxygen species metabolic process / regulation of glucose metabolic process / positive regulation of ATP biosynthetic process / regulation of protein ubiquitination / cellular response to unfolded protein / cullin family protein binding / regulation of synaptic vesicle endocytosis / protein deubiquitination / negative regulation of mitochondrial fission / protein monoubiquitination / 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 / central nervous system development / regulation of autophagy / Josephin domain DUBs / PINK1-PRKN Mediated Mitophagy
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 ...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 / IBR domain / : / 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
Water00
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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