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- PDB-9c5e: Covalent Complex Between Parkin Catalytic (Rcat) Domain and Ubiquitin -

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Basic information

Entry
Database: PDB / ID: 9c5e
TitleCovalent Complex Between Parkin Catalytic (Rcat) Domain and Ubiquitin
Components
  • E3 ubiquitin-protein ligase parkin
  • Polyubiquitin-B
KeywordsLIGASE / Covalent complex E3 ligase Thioether Haddock
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 / positive regulation of neuronal action potential / type 2 mitophagy ...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 / positive regulation of neuronal action potential / type 2 mitophagy / negative regulation of mitochondrial fusion / positive regulation of autophagy of mitochondrion / RBR-type E3 ubiquitin transferase / positive regulation of mitophagy / regulation of cellular response to oxidative stress / negative regulation of JNK cascade / mitochondrial fission / regulation of mitochondrion organization / ubiquitin conjugating enzyme binding / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / autophagy of mitochondrion / positive regulation of mitochondrial fission / oogenesis / female gonad development / seminiferous tubule development / male meiosis I / protein monoubiquitination / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / mitophagy / protein autoubiquitination / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / ubiquitin ligase complex / energy homeostasis / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Constitutive Signaling by NOTCH1 HD Domain Mutants / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / Regulation of FZD by ubiquitination / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / VLDLR internalisation and degradation / Pexophagy / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by POLK / neuron projection morphogenesis / adult locomotory behavior / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / InlB-mediated entry of Listeria monocytogenes into host cell / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / IKK complex recruitment mediated by RIP1 / negative regulation of protein phosphorylation / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / regulation of mitochondrial membrane potential / positive regulation of protein ubiquitination / TNFR1-induced NF-kappa-B 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 / IBR domain / E3 ubiquitin ligase RBR family ...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 ligase RBR family / IBR domain / In Between Ring fingers / TRIAD supradomain / TRIAD supradomain profile. / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Polyubiquitin-B / E3 ubiquitin-protein ligase parkin
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Homo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsConnelly, E.M. / Rintala-Dempsey, A.C. / Gundogdu, M. / Freeman, E.A. / Koszela, J. / Aguirre, J.D. / Zhu, G. / Kamarainen, O. / Tadayon, R. / Walden, H. / Shaw, G.S.
Funding support Canada, United Kingdom, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-14606 Canada
Wellcome Trust209347/Z/17/Z United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Capturing the catalytic intermediates of parkin ubiquitination.
Authors: Connelly, E.M. / Rintala-Dempsey, A.C. / Gundogdu, M. / Freeman, E.A. / Koszela, J. / Aguirre, J.D. / Zhu, G. / Kamarainen, O. / Tadayon, R. / Walden, H. / Shaw, G.S.
History
DepositionJun 6, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release
Revision 2.0Oct 9, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _pdbx_entry_details.has_protein_modification / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase parkin
B: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0514
Polymers16,9202
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1800 Å2
ΔGint-9 kcal/mol
Surface area8720 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 1000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein E3 ubiquitin-protein ligase parkin


Mass: 8280.427 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: park, parkin, CG10523 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q7KTX7, RBR-type E3 ubiquitin transferase
#2: Protein Polyubiquitin-B


Mass: 8639.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0CG47
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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
112isotropic13D HN(CA)CB
122isotropic13D CBCA(CO)NH
171isotropic13D HN(CA)CB
181isotropic13D HNCA
151isotropic12D 1H-15N HSQC
1121isotropic12D 1H-13C HSQC
133isotropic13D HN(CA)CB
143isotropic13D CBCA(CO)NH
1113isotropic13D HNCA
163isotropic12D 1H-15N HSQC
1133isotropic12D 1H-13C HSQC
194isotropic12D 1H-15N HSQC
1105isotropic12D 1H-15N HSQC

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution1300 uM [U-13C; U-15N] Rcat domain from Parkin, 300 uM Ubiquitin G75-C3, 90% H2O/10% D2ORcat-Ub Covalent complex with 13C,15N-labelled Rcat domain from fly parkin (aa 410-482) linked to unlabelled Ub G75-C3.13C,15N-Rcat-Ub90% H2O/10% D2O
solution2800 uM [U-13C; U-15N] Rcat domain from Parkin, 800 uM Ubiquitin G75-C3, 90% H2O/10% D2ORcat-Ub Covalent complex with 13C,15N-labelled Rcat domain from fly parkin (aa 410-482) linked to unlabelled Ub G75-C3.13C,15N-Rcat-Ub290% H2O/10% D2O
solution3300 uM [U-13C; U-15N] Ubiquitin G75-C3, 300 uM Rcat domain from Parkin, 90% H2O/10% D2ORcat-Ub Covalent complex with unlabelled Rcat domain from fly parkin (aa 410-482) linked to 13C,15N-labelled Ub G75-C3.Rcat-15N,13C-Ub90% H2O/10% D2O
solution4300 uM [U-13C; U-15N] Rcat domain from Parkin, 90% H2O/10% D2O13C,15N-Rcat domain from fly parkin (aa 410-482) in absence of Ub.13C,15N-Rcat90% H2O/10% D2O
solution5500 uM [U-13C; U-15N] Ubiquitin G75-C3, 90% H2O/10% D2O13C,15N-Ub G75-C3 in absence of Rcat.13C,15N-Ub-C390% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 uMRcat domain from Parkin[U-13C; U-15N]1
300 uMUbiquitin G75-C3natural abundance1
800 uMRcat domain from Parkin[U-13C; U-15N]2
800 uMUbiquitin G75-C3natural abundance2
300 uMUbiquitin G75-C3[U-13C; U-15N]3
300 uMRcat domain from Parkinnatural abundance3
300 uMRcat domain from Parkin[U-13C; U-15N]4
500 uMUbiquitin G75-C3[U-13C; U-15N]5
Sample conditionsDetails: 25 mM HEPES, 0.5 mM TCEP / Ionic strength: 100 mM / Label: Conditions_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
NameDeveloperClassification
NMRViewJJohnson and Blevinschemical shift assignment
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
HADDOCKBonvinstructure calculation
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 10

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