+Open data
-Basic information
Entry | Database: PDB / ID: 8ik6 | ||||||
---|---|---|---|---|---|---|---|
Title | pUbl depleted Parkin complex with pUbiquitin | ||||||
Components |
| ||||||
Keywords | LIGASE / E3 Ligase | ||||||
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 / regulation protein catabolic process at presynapse / negative regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway / 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 / regulation protein catabolic process at presynapse / negative regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway / 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 / Parkin-FBXW7-Cul1 ubiquitin ligase complex / negative regulation of actin filament bundle assembly / positive regulation of mitochondrial fusion / free ubiquitin chain polymerization / protein K29-linked ubiquitination / regulation of synaptic vesicle transport / negative regulation of mitochondrial fusion / : / positive regulation of protein linear polyubiquitination / F-box domain binding / RBR-type E3 ubiquitin transferase / negative regulation by host of viral genome replication / cellular response to toxic substance / positive regulation of mitophagy / regulation of necroptotic process / regulation of cellular response to oxidative stress / 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 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 / ubiquitin conjugating enzyme binding / aggresome assembly / autophagy of mitochondrion / regulation of mitochondrion organization / regulation of canonical Wnt signaling pathway / aggresome / regulation of reactive oxygen species metabolic process / regulation of synaptic vesicle endocytosis / positive regulation of DNA binding / protein deubiquitination / positive regulation of mitochondrial fission / dopamine uptake involved in synaptic transmission / ubiquitin-specific protease binding / regulation of dopamine secretion / dopamine metabolic process / negative regulation of release of cytochrome c from mitochondria / startle response / protein monoubiquitination / Peptide chain elongation / cullin family protein binding / phospholipase binding / Selenocysteine synthesis / protein K63-linked ubiquitination / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / regulation of protein ubiquitination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / regulation of glucose metabolic process / mitophagy / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of reactive oxygen species metabolic process / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / cellular response to unfolded protein / cellular response to manganese ion / protein autoubiquitination / proteasomal protein catabolic process / negative regulation of insulin secretion / protein K48-linked ubiquitination / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / ERAD pathway / ubiquitin ligase complex / cytosolic ribosome / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / FLT3 signaling by CBL mutants Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
Authors | Lenka, D.R. / Kumar, A. | ||||||
Funding support | India, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8ik6.cif.gz | 160.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8ik6.ent.gz | 120.7 KB | Display | PDB format |
PDBx/mmJSON format | 8ik6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ik6_validation.pdf.gz | 5.3 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8ik6_full_validation.pdf.gz | 5.4 MB | Display | |
Data in XML | 8ik6_validation.xml.gz | 29.5 KB | Display | |
Data in CIF | 8ik6_validation.cif.gz | 38.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ik/8ik6 ftp://data.pdbj.org/pub/pdb/validation_reports/ik/8ik6 | HTTPS FTP |
-Related structure data
Related structure data | 8ikmC 8iktC 8ikvC 8jwvC 5n2wS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | 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 | 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 / #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | Has protein modification | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.98 Å3/Da / Density % sol: 69.07 % |
---|---|
Crystal grow | Temperature: 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
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 29, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8856 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 3.3→3.56 Å / Num. unique obs: 4366 / CC1/2: 0.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.3→39.15 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|