[English] 日本語
Yorodumi
- PDB-6n13: UbcH7-Ub Complex with R0RBR Parkin and phosphoubiquitin -

+
Open data


ID or keywords:

Loading...

-
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


: / 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 / regulation of protein targeting to mitochondrion ...: / 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 / regulation of protein targeting to mitochondrion / negative regulation of glucokinase activity / negative regulation of exosomal secretion / mitochondrion to lysosome vesicle-mediated transport / type 2 mitophagy / response to curcumin / negative regulation of mitochondrial fusion / cell cycle phase transition / cellular response to hydrogen sulfide / protein K29-linked ubiquitination / free ubiquitin chain polymerization / Parkin-FBXW7-Cul1 ubiquitin ligase complex / positive regulation of protein linear polyubiquitination / Lewy body / host-mediated suppression of viral genome replication / ubiquitin-protein transferase activator activity / protein K27-linked ubiquitination / RBR-type E3 ubiquitin transferase / regulation of synaptic vesicle transport / F-box domain binding / positive regulation of mitochondrial fusion / positive regulation of mitophagy / negative regulation of actin filament bundle assembly / regulation of necroptotic process / mitochondrial fragmentation involved in apoptotic process / regulation of cellular response to oxidative stress / positive regulation of dendrite extension / negative regulation of excitatory postsynaptic potential / regulation of dopamine metabolic process / protein K6-linked ubiquitination / norepinephrine metabolic process / dopaminergic synapse / autophagy of mitochondrion / positive regulation of type 2 mitophagy / mitochondrion localization / protein localization to mitochondrion / positive regulation of proteasomal protein catabolic process / positive regulation of protein localization to membrane / cellular response to dopamine / cellular response to toxic substance / mitochondrial fission / positive regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / protein K11-linked ubiquitination / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / aggresome assembly / cellular response to L-glutamate / regulation of mitochondrion organization / ubiquitin conjugating enzyme binding / negative regulation of synaptic transmission, glutamatergic / hypothalamus gonadotrophin-releasing hormone neuron development / regulation of canonical Wnt signaling pathway / female meiosis I / positive regulation of protein monoubiquitination / negative regulation of JNK cascade / positive regulation of mitochondrial membrane potential / aggresome / positive regulation of protein targeting to mitochondrion / fat pad development / mitochondrion transport along microtubule / regulation of reactive oxygen species metabolic process / cellular response to glucocorticoid stimulus / E2 ubiquitin-conjugating enzyme / response to corticosterone / cellular response to steroid hormone stimulus / positive regulation of mitochondrial fission / female gonad development / seminiferous tubule development / response to muscle activity / negative regulation of release of cytochrome c from mitochondria / ubiquitin-specific protease binding / startle response / dopamine metabolic process / dopamine uptake involved in synaptic transmission / male meiosis I / regulation of dopamine secretion / ubiquitin conjugating enzyme activity / positive regulation of ATP biosynthetic process / negative regulation of reactive oxygen species metabolic process / regulation of glucose metabolic process / cullin family protein binding / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / regulation of protein ubiquitination / protein K63-linked ubiquitination / protein deubiquitination / cellular response to unfolded protein / protein monoubiquitination / regulation of synaptic vesicle endocytosis / ubiquitin ligase complex / negative regulation of mitochondrial fission / positive regulation of insulin secretion involved in cellular response to glucose stimulus
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-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. / : / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more