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- PDB-2m48: Solution Structure of IBR-RING2 Tandem Domain from Parkin -

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Basic information

Entry
Database: PDB / ID: 2m48
TitleSolution Structure of IBR-RING2 Tandem Domain from Parkin
ComponentsE3 UBIQUITIN-PROTEIN LIGASE PARKIN
KeywordsLIGASE / Parkin / RING / IBR / E3 ligase / Zn-binding
Function / homology
Function and homology information


positive regulation of compound eye pigmentation / positive regulation of locomotor rhythm / PINK1-PRKN Mediated Mitophagy / Josephin domain DUBs / sperm mitochondrion organization / larval locomotory behavior / Antigen processing: Ubiquitination & Proteasome degradation / Aggrephagy / parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization / positive regulation of neuronal action potential ...positive regulation of compound eye pigmentation / positive regulation of locomotor rhythm / PINK1-PRKN Mediated Mitophagy / Josephin domain DUBs / sperm mitochondrion organization / larval locomotory behavior / Antigen processing: Ubiquitination & Proteasome degradation / Aggrephagy / parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization / positive regulation of neuronal action potential / negative regulation of mitochondrial fusion / RBR-type E3 ubiquitin transferase / positive regulation of autophagy of mitochondrion / positive regulation of mitophagy / regulation of cellular response to oxidative stress / autophagy of mitochondrion / negative regulation of JNK cascade / mitochondrial fission / ubiquitin conjugating enzyme binding / regulation of mitochondrion organization / oogenesis / positive regulation of mitochondrial fission / protein monoubiquitination / protein autoubiquitination / ubiquitin ligase complex / mitochondrion organization / adult locomotory behavior / negative regulation of protein phosphorylation / neuron cellular homeostasis / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / ubiquitin-dependent protein catabolic process / spermatogenesis / regulation of apoptotic process / response to oxidative stress / protein ubiquitination / Golgi apparatus / endoplasmic reticulum / mitochondrion / zinc ion binding / cytosol / cytoplasm
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. / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
E3 ubiquitin-protein ligase parkin / E3 ubiquitin-protein ligase parkin
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsclosest to the average, model 11
AuthorsNoh, Y.J. / Mercier, P. / Spratt, D.E. / Shaw, G.S.
CitationJournal: Nat Commun / Year: 2013
Title: A molecular explanation for the recessive nature of parkin-linked Parkinson's disease.
Authors: Spratt, D.E. / Julio Martinez-Torres, R. / Noh, Y.J. / Mercier, P. / Manczyk, N. / Barber, K.R. / Aguirre, J.D. / Burchell, L. / Purkiss, A. / Walden, H. / Shaw, G.S.
History
DepositionJan 30, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Oct 15, 2014Group: Structure summary
Revision 1.3Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_nmr_software / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 15, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 UBIQUITIN-PROTEIN LIGASE PARKIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7225
Polymers15,4611
Non-polymers2624
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 / 20structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein E3 UBIQUITIN-PROTEIN LIGASE PARKIN


Mass: 15460.575 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Description: modified to have TEV site / Gene: CG10523, park / Production host: Escherichia coli (E. coli) / References: UniProt: Q95TI4, UniProt: Q7KTX7*PLUS
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / 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
1112D 1H-15N HSQC
1222D 1H-13C HSQC aliphatic
1313D 1H-15N NOESY
1433D (H)CCH-TOCSY
1533D 1H-13C NOESY aliphatic
1633D 1H-13C NOESY aromatic
1723D HNCA
1823D HCACO
1923D HN(CA)CB
11023D CBCA(CO)NH
11123D HNCO
11223D HNHA
11323D C(CO)NH
11423D 1H-13C NOESY aliphatic
11532D (HB)CB(CGCD)HD
11632D (HB)CB(CGCDCE)HE
11723D HNHB
11832D 1H-13C HSQC aromatic
11923D H(CCO)NH
12033D 13C TOCSY aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
125 mM TRIS, 150 mM sodium chloride, 5 mM DTT, 500 uM [U-98% 15N] SD01679p, 90% H2O/10% D2O90% H2O/10% D2O
225 mM TRIS, 150 mM sodium chloride, 5 mM DTT, 500 uM [U-98% 13C; U-98% 15N] SD01679p, 90% H2O/10% D2O90% H2O/10% D2O
325 mM TRIS, 150 mM sodium chloride-, 5 mM DTT, 500 uM [U-98% 13C; U-98% 15N] SD01679p, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
25 mMTRIS-11
150 mMsodium chloride-21
5 mMDTT-31
500 uMentity_1-4[U-98% 15N]1
25 mMTRIS-52
150 mMsodium chloride-62
5 mMDTT-72
500 uMentity_1-8[U-98% 13C; U-98% 15N]2
25 mMTRIS-93
150 mMsodium chloride-103
5 mMDTT-113
500 uMentity_1-12[U-98% 13C; U-98% 15N]3
Sample conditionsIonic strength: 0.150 / pH: 7.5 / Pressure: ambient / 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
VnmrJVarian VnmrJ 2.2DVariancollection
NMRPipe2011.084.20.33Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawVer 5.7 Rev 2011.084.20.33Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRView8.2.33 with Java 1.6.0_31Johnson, One Moon Scientificdata analysis
NMRView8.2.33 with Java 1.6.0_31Johnson, One Moon Scientificchemical shift assignment
NMRView8.2.33 with Java 1.6.0_31Johnson, One Moon Scientificpeak picking
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
X-PLOR NIH2.33Schwieters, Kuszewski, Tjandra and Clorerefinement
TALOSTALOSPlusCornilescu, Delaglio and Baxgeometry optimization
Procheck3.5.4Laskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thodata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1 / Details: with explicit solvent and full electrostatics
NMR constraintsNOE constraints total: 1204 / NOE intraresidue total count: 360 / NOE long range total count: 328 / NOE medium range total count: 115 / NOE sequential total count: 353 / Protein chi angle constraints total count: 321 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 49 / Protein psi angle constraints total count: 49
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 20 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum torsion angle constraint violation: 7.5 ° / Maximum upper distance constraint violation: 0.7 Å
NMR ensemble rmsDistance rms dev: 0.04 Å / Distance rms dev error: 0.002 Å

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