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- PDB-8ikm: Trans complex of phospho parkin -

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Basic information

Entry
Database: PDB / ID: 8ikm
TitleTrans complex of phospho parkin
Components
  • (E3 ubiquitin-protein ligase ...) x 2
  • 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 / regulation of protein targeting to mitochondrion / cellular response to L-glutamine ...: / 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 / regulation of protein targeting to mitochondrion / cellular response to L-glutamine / negative regulation of exosomal secretion / negative regulation of glucokinase activity / mitochondrion to lysosome vesicle-mediated transport / type 2 mitophagy / response to curcumin / cellular response to hydrogen sulfide / protein K27-linked ubiquitination / negative regulation of mitochondrial fusion / Parkin-FBXW7-Cul1 ubiquitin ligase complex / protein K29-linked ubiquitination / free ubiquitin chain polymerization / Lewy body / positive regulation of protein linear polyubiquitination / negative regulation of actin filament bundle assembly / host-mediated suppression of viral genome replication / RBR-type E3 ubiquitin transferase / regulation of synaptic vesicle transport / positive regulation of mitophagy / F-box domain binding / positive regulation of mitochondrial fusion / regulation of cellular response to oxidative stress / regulation of necroptotic process / mitochondrial fragmentation involved in apoptotic process / mitochondrion localization / positive regulation of dendrite extension / regulation of dopamine metabolic process / negative regulation of excitatory postsynaptic potential / protein K6-linked ubiquitination / dopaminergic synapse / norepinephrine metabolic process / autophagy of mitochondrion / positive regulation of type 2 mitophagy / protein localization to mitochondrion / response to insecticide / positive regulation of proteasomal protein catabolic process / cellular response to dopamine / positive regulation of protein localization to membrane / cellular response to toxic substance / mitochondrial fission / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / positive regulation of tumor necrosis factor-mediated signaling pathway / aggresome assembly / protein K11-linked ubiquitination / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / cellular response to L-glutamate / negative regulation of synaptic transmission, glutamatergic / regulation of mitochondrion organization / ubiquitin conjugating enzyme binding / regulation of canonical Wnt signaling pathway / positive regulation of mitochondrial membrane potential / negative regulation of JNK cascade / aggresome / regulation of reactive oxygen species metabolic process / response to corticosterone / positive regulation of mitochondrial fission / dopamine uptake involved in synaptic transmission / ubiquitin-specific protease binding / response to muscle activity / negative regulation of release of cytochrome c from mitochondria / regulation of dopamine secretion / startle response / dopamine metabolic process / positive regulation of ATP biosynthetic process / cullin family protein binding / negative regulation of reactive oxygen species metabolic process / Peptide chain elongation / Selenocysteine synthesis / regulation of glucose metabolic process / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / protein K63-linked ubiquitination / protein deubiquitination / Viral mRNA Translation / regulation of synaptic vesicle endocytosis / regulation of protein ubiquitination / Maturation of protein E / protein monoubiquitination / Maturation of protein E / negative regulation of mitochondrial fission / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / cellular response to unfolded protein / GTP hydrolysis and joining of the 60S ribosomal subunit / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / ubiquitin ligase complex / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / L13a-mediated translational silencing of Ceruloplasmin expression
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 / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / 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: 1.92 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

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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: Ubiquitin
C: E3 ubiquitin-protein ligase parkin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,79311
Polymers52,2023
Non-polymers5918
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-21 kcal/mol
Surface area18130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.804, 83.804, 105.033
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-124-

HOH

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Components

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E3 ubiquitin-protein ligase ... , 2 types, 2 molecules AC

#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: 27508.426 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 BL21(DE3) (bacteria)
References: UniProt: O60260, RBR-type E3 ubiquitin transferase
#3: 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: 16093.925 Da / Num. of mol.: 1
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

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Protein , 1 types, 1 molecules B

#2: Protein Ubiquitin


Mass: 8599.758 Da / Num. of mol.: 1
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

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Non-polymers , 4 types, 104 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.3 M Sodium nitrate, 0.3 Sodium phosphate dibasic, 0.3 M Ammonium sulfate,1.0 M 8.5 Tris (base), BICINE, 25% v/v MPD; 25% PEG 1000, 25% w/v PEG 3350

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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: 1.92→42.6 Å / Num. obs: 33029 / % possible obs: 99.7 % / Redundancy: 5.6 % / CC1/2: 0.998 / Net I/σ(I): 13.7
Reflection shellResolution: 1.92→1.97 Å / Num. unique obs: 2167 / CC1/2: 0.724

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GLC

6glc


Resolution: 1.92→42.6 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.96 / SU B: 12.418 / SU ML: 0.149 / Cross valid method: FREE R-VALUE / ESU R: 0.357 / ESU R Free: 0.142
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2325 1675 5.077 %
Rwork0.2048 31316 -
all0.206 --
obs-31316 99.635 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 60.224 Å2
Baniso -1Baniso -2Baniso -3
1--0.904 Å2-0.452 Å20 Å2
2---0.904 Å2-0 Å2
3---2.933 Å2
Refinement stepCycle: LAST / Resolution: 1.92→42.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2911 0 19 96 3026
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0123013
X-RAY DIFFRACTIONr_angle_refined_deg0.8291.6394086
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6985385
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.93322.745153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.32215500
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9141518
X-RAY DIFFRACTIONr_chiral_restr0.0720.2396
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022292
X-RAY DIFFRACTIONr_nbd_refined0.1910.21274
X-RAY DIFFRACTIONr_nbtor_refined0.3020.22047
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2159
X-RAY DIFFRACTIONr_metal_ion_refined0.0290.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2520.231
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1460.214
X-RAY DIFFRACTIONr_mcbond_it3.6995.9351515
X-RAY DIFFRACTIONr_mcangle_it5.058.8981891
X-RAY DIFFRACTIONr_scbond_it3.8216.191497
X-RAY DIFFRACTIONr_scangle_it4.9969.1532188
X-RAY DIFFRACTIONr_lrange_it7.15980.2174372
X-RAY DIFFRACTIONr_rigid_bond_restr0.83933012
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.970.3591400.3172246X-RAY DIFFRACTION99.5826
1.97-2.0240.3571190.2732208X-RAY DIFFRACTION99.487
2.024-2.0830.2731070.2622185X-RAY DIFFRACTION99.6955
2.083-2.1470.2951090.2452121X-RAY DIFFRACTION99.6425
2.147-2.2170.2541090.2252044X-RAY DIFFRACTION99.8146
2.217-2.2950.2611010.2051970X-RAY DIFFRACTION99.7591
2.295-2.3810.2511070.1981937X-RAY DIFFRACTION99.9511
2.381-2.4790.2641020.2041840X-RAY DIFFRACTION99.7432
2.479-2.5890.2521200.2041755X-RAY DIFFRACTION100
2.589-2.7150.247880.211703X-RAY DIFFRACTION99.8328
2.715-2.8620.278870.2231611X-RAY DIFFRACTION99.7064
2.862-3.0350.28810.2021525X-RAY DIFFRACTION99.7515
3.035-3.2450.234700.21463X-RAY DIFFRACTION99.9348
3.245-3.5040.263760.2091350X-RAY DIFFRACTION99.0278
3.504-3.8380.251440.1931275X-RAY DIFFRACTION99.7731
3.838-4.2910.241570.1951128X-RAY DIFFRACTION99.9157
6.063-8.560.225360.213682X-RAY DIFFRACTION99.0345

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