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- PDB-6n13: UbcH7-Ub Complex with R0RBR Parkin and phosphoubiquitin -

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Basic information

Entry
Database: PDB / ID: 6n13
TitleUbcH7-Ub Complex with R0RBR Parkin and phosphoubiquitin
Components
  • E3 ubiquitin-protein ligase parkin
  • Ubiquitin-conjugating enzyme E2 L3
  • phosphoubiquitin
  • ubiquitin
KeywordsLIGASE / E3 enzyme / protein degradation / mitochondrial protein
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 / negative regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway / regulation protein catabolic process at presynapse / regulation of protein targeting to mitochondrion / negative regulation of spontaneous neurotransmitter secretion / 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 / negative regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway / regulation protein catabolic process at presynapse / regulation of protein targeting to mitochondrion / negative regulation of spontaneous neurotransmitter secretion / negative regulation of intralumenal vesicle formation / negative regulation of glucokinase activity / negative regulation of exosomal secretion / mitochondrion to lysosome vesicle-mediated transport / type 2 mitophagy / Lewy body / protein K27-linked ubiquitination / negative regulation of actin filament bundle assembly / Parkin-FBXW7-Cul1 ubiquitin ligase complex / free ubiquitin chain polymerization / cell cycle phase transition / regulation of synaptic vesicle transport / negative regulation of mitochondrial fusion / protein K29-linked ubiquitination / : / positive regulation of protein linear polyubiquitination / ubiquitin-protein transferase activator activity / RBR-type E3 ubiquitin transferase / negative regulation by host of viral genome replication / F-box domain binding / positive regulation of mitochondrial fusion / positive regulation of mitophagy / regulation of cellular response to oxidative stress / regulation of necroptotic process / regulation of dopamine metabolic process / dopaminergic synapse / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / cellular response to toxic substance / positive regulation of dendrite extension / protein K6-linked ubiquitination / positive regulation of proteasomal protein catabolic process / norepinephrine metabolic process / protein localization to mitochondrion / positive regulation of protein localization to membrane / negative regulation of JNK cascade / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / positive regulation of tumor necrosis factor-mediated signaling pathway / cellular response to dopamine / mitochondrial fission / protein K11-linked ubiquitination / aggresome assembly / regulation of mitochondrion organization / ubiquitin conjugating enzyme binding / hypothalamus gonadotrophin-releasing hormone neuron development / regulation of canonical Wnt signaling pathway / aggresome / female meiosis I / positive regulation of ubiquitin-protein transferase activity / regulation of reactive oxygen species metabolic process / positive regulation of protein monoubiquitination / regulation of synaptic vesicle endocytosis / positive regulation of protein targeting to mitochondrion / cellular response to glucocorticoid stimulus / fat pad development / mitochondrion transport along microtubule / autophagy of mitochondrion / cellular response to steroid hormone stimulus / E2 ubiquitin-conjugating enzyme / positive regulation of DNA binding / positive regulation of mitochondrial fission / dopamine uptake involved in synaptic transmission / regulation of dopamine secretion / female gonad development / ubiquitin-specific protease binding / seminiferous tubule development / negative regulation of release of cytochrome c from mitochondria / male meiosis I / startle response / dopamine metabolic process / protein monoubiquitination / ubiquitin conjugating enzyme activity / cullin family protein binding / phospholipase binding / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / protein K63-linked ubiquitination / regulation of protein ubiquitination / regulation of glucose metabolic process / mitophagy / protein deubiquitination / negative regulation of reactive oxygen species metabolic process / cellular response to unfolded protein / cellular response to manganese ion / negative regulation of insulin secretion / proteasomal protein catabolic process / protein autoubiquitination / protein K48-linked ubiquitination / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / ubiquitin ligase complex / energy homeostasis / ERAD 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 Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / 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 / Polyubiquitin-B / Polyubiquitin-C / Ubiquitin-conjugating enzyme E2 L3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsCondos, T.E.C. / Dunkerley, K.M. / Freeman, E.A. / Barber, K.R. / Aguirre, J.D. / Chaugule, V.K. / Xiao, Y. / Konermann, L. / Walden, H. / Shaw, G.S.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-14606 Canada
Citation
Journal: EMBO J. / Year: 2018
Title: Synergistic recruitment of UbcH7~Ub and phosphorylated Ubl domain triggers parkin activation.
Authors: Condos, T.E. / Dunkerley, K.M. / Freeman, E.A. / Barber, K.R. / Aguirre, J.D. / Chaugule, V.K. / Xiao, Y. / Konermann, L. / Walden, H. / Shaw, G.S.
#1: Journal: Nat. Struct. Mol. Biol. / Year: 2017
Title: Parkin-phosphoubiquitin complex reveals cryptic ubiquitin-binding site required for RBR ligase activity.
Authors: Kumar, A. / Chaugule, V.K. / Condos, T.E.C. / Barber, K.R. / Johnson, C. / Toth, R. / Sundaramoorthy, R. / Knebel, A. / Shaw, G.S. / Walden, H.
History
DepositionNov 8, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Data collection / Database references
Category: pdbx_audit_support / pdbx_nmr_software / struct_ref_seq_dif
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: E3 ubiquitin-protein ligase parkin
D: ubiquitin
C: Ubiquitin-conjugating enzyme E2 L3
A: phosphoubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,88612
Polymers71,3634
Non-polymers5238
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area4990 Å2
ΔGint-81 kcal/mol
Surface area32500 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 / Parkin / Parkin RBR E3 ubiquitin-protein ligase / Parkinson juvenile disease protein 2 / Parkinson ...Parkin / Parkin RBR E3 ubiquitin-protein ligase / Parkinson juvenile disease protein 2 / Parkinson disease protein 2


Mass: 36050.219 Da / Num. of mol.: 1 / Mutation: Q347C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKN, PARK2 / Production host: Escherichia coli (E. coli)
References: UniProt: O60260, RBR-type E3 ubiquitin transferase
#2: Protein ubiquitin


Mass: 8576.831 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 (E. coli) / References: UniProt: P0CG47
#3: Protein Ubiquitin-conjugating enzyme E2 L3 / E2 ubiquitin-conjugating enzyme L3 / L-UBC / UbcH7 / Ubiquitin carrier protein L3 / Ubiquitin- ...E2 ubiquitin-conjugating enzyme L3 / L-UBC / UbcH7 / Ubiquitin carrier protein L3 / Ubiquitin-conjugating enzyme E2-F1 / Ubiquitin-protein ligase L3


Mass: 18078.699 Da / Num. of mol.: 1 / Mutation: C17S, C86K, C137S
Source method: isolated from a genetically manipulated source
Details: GH residues at N-terminus were used in the expression construct but were not included in the x-ray coordinates
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2L3, UBCE7, UBCH7 / Production host: Escherichia coli (E. coli)
References: UniProt: P68036, E2 ubiquitin-conjugating enzyme
#4: Protein phosphoubiquitin


Mass: 8656.811 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentSample state: isotropic / Type: 2D 1H-15N HSQC

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Sample preparation

DetailsType: solution
Contents: 0.11 mM [U-13C; U-15N; U-2H] UbcH7, 0.11 mM [U-13C; U-15N; U-2H] ubiquitin, 0.11 mM [U-2H] Parkin -residues 144-465 comprising the RING0-RING1-IBR and RING2(Rcat) domains, 0.11 mM [U-2H] ...Contents: 0.11 mM [U-13C; U-15N; U-2H] UbcH7, 0.11 mM [U-13C; U-15N; U-2H] ubiquitin, 0.11 mM [U-2H] Parkin -residues 144-465 comprising the RING0-RING1-IBR and RING2(Rcat) domains, 0.11 mM [U-2H] phosphorylated ubiquitin, 90% H2O/10% D2O
Details: 2H phosphorylated ubiquitin:parkin complex was titrated into the covalent UbcH7-Ub complex
Label: Sample 1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.11 mMUbcH7[U-13C; U-15N; U-2H]1
0.11 mMubiquitin[U-13C; U-15N; U-2H]1
0.11 mMParkin -residues 144-465 comprising the RING0-RING1-IBR and RING2(Rcat) domains[U-2H]1
0.11 mMphosphorylated ubiquitin[U-2H]1
Sample conditionsIonic strength: 50 mM / Label: Sample 1 / pH: 7 / PH err: 0.05 / Pressure: ambient atm / Temperature: 298 K / Temperature err: 0.1

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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
HADDOCKBonvinstructure calculation
NMRViewJohnson, One Moon Scientificpeak picking
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PyMOL2.0.0Schrodinger LLCgeometry optimization
RefinementMethod: simulated annealing / Software ordinal: 1
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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