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- PDB-8jwv: Untethered R0RBR -

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Basic information

Entry
Database: PDB / ID: 8jwv
TitleUntethered R0RBR
ComponentsE3 ubiquitin-protein ligase parkin
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 / negative regulation of exosomal secretion ...: / 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 / negative regulation of exosomal secretion / negative regulation of glucokinase activity / mitochondrion to lysosome vesicle-mediated transport / type 2 mitophagy / Lewy body / negative regulation of actin filament bundle assembly / protein K27-linked ubiquitination / negative regulation of mitochondrial fusion / Parkin-FBXW7-Cul1 ubiquitin ligase complex / protein K29-linked ubiquitination / free ubiquitin chain polymerization / positive regulation of protein linear polyubiquitination / negative regulation by host of viral genome replication / positive regulation of mitophagy / RBR-type E3 ubiquitin transferase / regulation of synaptic vesicle transport / F-box domain binding / positive regulation of mitochondrial fusion / regulation of cellular response to oxidative stress / regulation of necroptotic process / regulation of dopamine metabolic process / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / dopaminergic synapse / positive regulation of dendrite extension / protein K6-linked ubiquitination / positive regulation of protein localization to membrane / autophagy of mitochondrion / norepinephrine metabolic process / cellular response to toxic substance / positive regulation of type 2 mitophagy / protein localization to mitochondrion / positive regulation of proteasomal protein catabolic process / cellular response to dopamine / negative regulation of JNK cascade / mitochondrial fission / positive regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / aggresome assembly / protein K11-linked ubiquitination / ubiquitin conjugating enzyme binding / regulation of mitochondrion organization / regulation of canonical Wnt signaling pathway / aggresome / regulation of reactive oxygen species metabolic process / positive regulation of mitochondrial fission / dopamine uptake involved in synaptic transmission / ubiquitin-specific protease binding / negative regulation of release of cytochrome c from mitochondria / regulation of dopamine secretion / startle response / dopamine metabolic process / phospholipase binding / regulation of synaptic vesicle endocytosis / cullin family protein binding / negative regulation of reactive oxygen species metabolic process / regulation of glucose metabolic process / protein K63-linked ubiquitination / protein deubiquitination / protein monoubiquitination / regulation of protein ubiquitination / cellular response to manganese ion / ubiquitin ligase complex / cellular response to unfolded protein / negative regulation of insulin secretion / proteasomal protein catabolic process / protein K48-linked ubiquitination / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / protein autoubiquitination / mitophagy / ERAD pathway / heat shock protein binding / Hsp70 protein binding / tubulin binding / response to endoplasmic reticulum stress / regulation of mitochondrial membrane potential / adult locomotory behavior / central nervous system development / Josephin domain DUBs / ubiquitin binding / learning / PINK1-PRKN Mediated Mitophagy / synaptic transmission, glutamatergic / PDZ domain binding / mitochondrion organization / macroautophagy / G protein-coupled receptor binding / negative regulation of canonical Wnt signaling pathway / protein destabilization / regulation of protein stability / beta-catenin binding / SH3 domain binding
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 family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
: / E3 ubiquitin-protein ligase parkin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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
DepositionJun 29, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Sep 18, 2024Group: Database references / Category: citation / citation_author

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,49312
Polymers36,6481
Non-polymers84511
Water32418
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.672, 132.579, 64.692
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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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: 36647.922 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 (E. coli)
References: UniProt: O60260, RBR-type E3 ubiquitin transferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ba / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.54 Å3/Da / Density % sol: 51.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES, pH 7.5, 8% PEG 4000, 10% isopropanol, 0.1 M BaCl2

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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: 2.9→64.69 Å / Num. obs: 8503 / % possible obs: 99.4 % / Redundancy: 3.8 % / CC1/2: 0.993 / Net I/σ(I): 11
Reflection shellResolution: 2.9→3.08 Å / Num. unique obs: 1360 / CC1/2: 0.924

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I1H

4i1h


Resolution: 2.9→48.33 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.882 / SU B: 13.672 / SU ML: 0.265 / Cross valid method: FREE R-VALUE / ESU R Free: 0.413 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2537 434 5.111 %
Rwork0.217 8058 -
all0.219 --
obs-8492 98.917 %
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: 44.299 Å2
Baniso -1Baniso -2Baniso -3
1--3.584 Å20 Å2-0 Å2
2--2.942 Å20 Å2
3---0.643 Å2
Refinement stepCycle: LAST / Resolution: 2.9→48.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2390 0 21 19 2430
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122500
X-RAY DIFFRACTIONr_angle_refined_deg1.6671.6753377
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9425304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.983519
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.16710403
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.72610117
X-RAY DIFFRACTIONr_chiral_restr0.0740.2351
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021893
X-RAY DIFFRACTIONr_nbd_refined0.2380.21043
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21846
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.281
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3510.269
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.8410.215
X-RAY DIFFRACTIONr_mcbond_it3.8234.291219
X-RAY DIFFRACTIONr_mcangle_it6.0377.7091519
X-RAY DIFFRACTIONr_scbond_it4.9594.491281
X-RAY DIFFRACTIONr_scangle_it7.338.1261857
X-RAY DIFFRACTIONr_lrange_it16.81146.269420788
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.9750.318360.272574X-RAY DIFFRACTION99.5106
2.975-3.0560.283360.28573X-RAY DIFFRACTION99.6727
3.056-3.1440.25290.25557X-RAY DIFFRACTION99.8296
3.144-3.2410.299190.231559X-RAY DIFFRACTION99.6552
3.241-3.3470.251330.214507X-RAY DIFFRACTION99.0826
3.347-3.4630.24260.235510X-RAY DIFFRACTION99.0758
3.463-3.5940.2370.2472X-RAY DIFFRACTION97.6967
3.594-3.7390.21290.21472X-RAY DIFFRACTION99.0119
3.739-3.9050.25270.185448X-RAY DIFFRACTION99.1649
3.905-4.0940.232210.19450X-RAY DIFFRACTION99.3671
4.094-4.3140.18160.18415X-RAY DIFFRACTION99.0805
4.314-4.5730.247210.183390X-RAY DIFFRACTION99.7573
4.886-5.2730.333210.183336X-RAY DIFFRACTION99.4429
5.273-5.7690.331150.225326X-RAY DIFFRACTION98.2709
6.438-7.4130.24680.246268X-RAY DIFFRACTION96.8421
7.413-9.0260.328120.235229X-RAY DIFFRACTION99.177
12.55-48.330.69970.307112X-RAY DIFFRACTION92.2481

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