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- PDB-8ik6: pUbl depleted Parkin complex with pUbiquitin -

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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 / 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 / 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 / Viral mRNA Translation / protein deubiquitination / protein monoubiquitination / regulation of protein ubiquitination / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / cellular response to manganese ion / ubiquitin ligase complex / cellular response to unfolded protein / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / negative regulation of insulin secretion / proteasomal protein catabolic process / 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) / protein autoubiquitination / mitophagy / ERAD pathway / heat shock protein binding / Maturation of protein E / Maturation of protein E / cytosolic ribosome / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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 / 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

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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: 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

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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: 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

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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

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