[English] 日本語
Yorodumi
- PDB-8ik6: pUbl depleted Parkin complex with pUbiquitin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ik6
TitlepUbl depleted Parkin complex with pUbiquitin
Components
  • E3 ubiquitin-protein ligase parkin
  • Ubiquitin
KeywordsLIGASE / E3 Ligase
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 exosomal secretion / negative regulation of glucokinase activity / mitochondrion to lysosome vesicle-mediated transport / type 2 mitophagy / response to curcumin / negative regulation of mitochondrial fusion / cellular response to hydrogen sulfide / Parkin-FBXW7-Cul1 ubiquitin ligase complex / protein K29-linked ubiquitination / free ubiquitin chain polymerization / Lewy body / positive regulation of protein linear polyubiquitination / host-mediated suppression of viral genome replication / protein K27-linked ubiquitination / RBR-type E3 ubiquitin transferase / regulation of synaptic vesicle transport / positive regulation of mitophagy / F-box domain binding / positive regulation of mitochondrial fusion / 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 / regulation of dopamine metabolic process / negative regulation of excitatory postsynaptic potential / protein K6-linked ubiquitination / norepinephrine metabolic process / dopaminergic synapse / autophagy of mitochondrion / positive regulation of type 2 mitophagy / mitochondrion localization / protein localization to mitochondrion / response to insecticide / cellular response to dopamine / positive regulation of proteasomal protein catabolic process / positive regulation of protein localization to membrane / cellular response to toxic substance / mitochondrial fission / positive regulation of tumor necrosis factor-mediated signaling pathway / protein K11-linked ubiquitination / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / aggresome assembly / cellular response to L-glutamate / regulation of mitochondrion organization / negative regulation of synaptic transmission, glutamatergic / ubiquitin conjugating enzyme binding / regulation of canonical Wnt signaling pathway / negative regulation of JNK cascade / aggresome / positive regulation of mitochondrial membrane potential / regulation of reactive oxygen species metabolic process / response to corticosterone / positive regulation of mitochondrial fission / 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 / regulation of dopamine secretion / positive regulation of ATP biosynthetic process / Peptide chain elongation / negative regulation of reactive oxygen species metabolic process / Selenocysteine synthesis / cullin family protein binding / regulation of glucose metabolic process / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / Viral mRNA Translation / regulation of protein ubiquitination / protein K63-linked ubiquitination / protein deubiquitination / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / protein monoubiquitination / cellular response to unfolded protein / GTP hydrolysis and joining of the 60S ribosomal subunit / ubiquitin ligase complex / regulation of synaptic vesicle endocytosis / L13a-mediated translational silencing of Ceruloplasmin expression / negative regulation of mitochondrial fission / positive regulation of insulin secretion involved in cellular response to glucose stimulus / Major pathway of rRNA processing in the nucleolus and cytosol / regulation of postsynaptic membrane neurotransmitter receptor levels / protein K48-linked ubiquitination / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)
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. / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
E3 ubiquitin-protein ligase parkin / Ubiquitin-ribosomal protein eL40 fusion protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsLenka, D.R. / Kumar, A.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)Innovative Young Biotechnology Award (DBT/12/IYBAl2019/03) and Ramalingaswami Fellowship (DBT/RLF/Re-entry/42/2019) India
Citation
Journal: Elife / Year: 2024
Title: Additional feedforward mechanism of Parkin activation via binding of phospho-UBL and RING0 in trans.
Authors: Lenka, D.R. / Dahe, S.V. / Antico, O. / Sahoo, P. / Prescott, A.R. / Muqit, M.M.K. / Kumar, A.
#1: Journal: Elife / Year: 2024
Title: Additional feedforward mechanism of Parkin activation via binding of phospho-UBL and RING0 in trans
Authors: Lenka, D. / Dahe, S. / Antico, O. / Sahoo, P. / Prescott, A.R. / Muqit, M.M.K. / Kumar, A.
History
DepositionFeb 28, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2024Group: Database references / Category: citation / citation_author
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: E3 ubiquitin-protein ligase parkin
D: Ubiquitin
A: E3 ubiquitin-protein ligase parkin
B: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,58427
Polymers90,8044
Non-polymers1,78023
Water362
1
C: E3 ubiquitin-protein ligase parkin
D: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,59817
Polymers45,4022
Non-polymers1,19615
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-141 kcal/mol
Surface area18580 Å2
MethodPISA
2
A: E3 ubiquitin-protein ligase parkin
B: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,98610
Polymers45,4022
Non-polymers5858
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-31 kcal/mol
Surface area16100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.805, 187.805, 141.857
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422

-
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 / Parkin R0RBR


Mass: 36802.086 Da / Num. of mol.: 2 / Mutation: R140P,Q347C,A383N,S384L,G385Y,T386F,T387Q,T388S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKN, PARK2 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O60260, RBR-type E3 ubiquitin transferase
#2: Protein Ubiquitin


Mass: 8599.758 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBA52, UBCEP2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P62987
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.98 Å3/Da / Density % sol: 69.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 1.6 M Ammonium sulfate, 0.1 M MES monohydrate pH 6.5, 10% v/v 1,4-Dioxane

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 3.3→39.15 Å / Num. obs: 20948 / % possible obs: 92.85 % / Redundancy: 7.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.1928 / Net I/σ(I): 8.4
Reflection shellResolution: 3.3→3.56 Å / Num. unique obs: 4366 / CC1/2: 0.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N2W

5n2w


Resolution: 3.3→39.15 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.93 / SU B: 31.9 / SU ML: 0.457 / Cross valid method: FREE R-VALUE / ESU R Free: 0.491
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.26985 --
Rwork0.23415 19853 -
all0.236 --
obs-19853 92.01 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.932 Å21.466 Å20 Å2
2--2.932 Å2-0 Å2
3----9.511 Å2
Refinement stepCycle: LAST / Resolution: 3.3→39.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5457 0 59 2 5518
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0125673
X-RAY DIFFRACTIONr_angle_refined_deg1.0611.6647684
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5915687
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.81122.007294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.40315924
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2651539
X-RAY DIFFRACTIONr_chiral_restr0.0730.2724
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024304
X-RAY DIFFRACTIONr_nbd_refined0.2020.22260
X-RAY DIFFRACTIONr_nbtor_refined0.3030.23748
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2125
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2860.253
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1310.25
X-RAY DIFFRACTIONr_mcbond_it5.12314.882781
X-RAY DIFFRACTIONr_mcangle_it8.48422.3123457
X-RAY DIFFRACTIONr_scbond_it5.96815.2042889
X-RAY DIFFRACTIONr_scangle_it9.12922.6544226
X-RAY DIFFRACTIONr_lrange_it13.673199.137879
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.3860.419780.4191493X-RAY DIFFRACTION95.5015
3.479-3.5790.38720.3471409X-RAY DIFFRACTION95.18
3.579-3.690.325810.3251348X-RAY DIFFRACTION94.0132
3.69-3.8110.362620.2961312X-RAY DIFFRACTION94.1096
3.811-3.9440.358560.2771294X-RAY DIFFRACTION93.9457
3.944-4.0930.317720.2511199X-RAY DIFFRACTION92.571
4.093-4.260.268720.2181165X-RAY DIFFRACTION93.5703
4.26-4.4490.28490.2091153X-RAY DIFFRACTION93.1783
4.449-4.6660.266640.2061068X-RAY DIFFRACTION92.4837
4.666-4.9180.311460.1951028X-RAY DIFFRACTION91.3265
4.918-5.2170.317590.215947X-RAY DIFFRACTION89.7413
5.217-5.5760.241650.203866X-RAY DIFFRACTION89.6917
5.576-6.0220.219420.216835X-RAY DIFFRACTION88.8551
6.022-6.5960.22480.205761X-RAY DIFFRACTION89.1952
6.596-7.3730.242320.214710X-RAY DIFFRACTION88.4386

+
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