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- PDB-8ikv: pUbl depleted phospho-Parkin(K211N,R163D) in complex with pUb -

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Basic information

Entry
Database: PDB / ID: 8ikv
TitlepUbl depleted phospho-Parkin(K211N,R163D) in complex with pUb
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 / 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 / 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 / mitochondrial fragmentation involved in apoptotic process / mitochondrion localization / regulation of dopamine metabolic process / positive regulation of dendrite extension / negative regulation of excitatory postsynaptic potential / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / protein K6-linked ubiquitination / dopaminergic synapse / norepinephrine metabolic process / autophagy of mitochondrion / positive regulation of type 2 mitophagy / protein localization to mitochondrion / cellular response to L-glutamate / 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 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 / regulation of glucose metabolic process / Selenocysteine synthesis / 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 / cellular response to manganese ion / 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) / ubiquitin ligase complex / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion
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: 2.35 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
DepositionMar 1, 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 23, 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
A: E3 ubiquitin-protein ligase parkin
B: Ubiquitin
D: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,58623
Polymers90,2214
Non-polymers1,36519
Water4,648258
1
C: E3 ubiquitin-protein ligase parkin
D: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,84612
Polymers45,1102
Non-polymers73610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-12 kcal/mol
Surface area19550 Å2
MethodPISA
2
A: E3 ubiquitin-protein ligase parkin
B: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,74011
Polymers45,1102
Non-polymers6299
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-20 kcal/mol
Surface area19760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.450, 76.426, 114.329
Angle α, β, γ (deg.)90.000, 100.485, 90.000
Int Tables number4
Space group name H-MP1211

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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: 36510.609 Da / Num. of mol.: 2 / Mutation: R140P,R163D,K211N,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
#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.: 16 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 2.16 Å3/Da / Density % sol: 43.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.15 M Potassium bromide, 30% w/v Polyethylene glycol monomethyl ether 2,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.35→38.39 Å / Num. obs: 31088 / % possible obs: 96.5 % / Redundancy: 3.1 % / CC1/2: 0.995 / Net I/σ(I): 7.7
Reflection shellResolution: 2.35→2.43 Å / Num. unique obs: 3040 / CC1/2: 0.686

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Processing

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

5caw


Resolution: 2.35→38.242 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.938 / SU B: 8.048 / SU ML: 0.185 / Cross valid method: FREE R-VALUE / ESU R: 0.585 / ESU R Free: 0.243
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2169 1512 4.866 %
Rwork0.1981 29561 -
all0.199 --
obs-29561 96.318 %
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: 44.93 Å2
Baniso -1Baniso -2Baniso -3
1-1.223 Å2-0 Å2-0.211 Å2
2--1.811 Å20 Å2
3----2.766 Å2
Refinement stepCycle: LAST / Resolution: 2.35→38.242 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6029 0 37 258 6324
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0126189
X-RAY DIFFRACTIONr_angle_refined_deg0.8361.6448377
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3195766
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.74522.209335
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.574151033
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5461544
X-RAY DIFFRACTIONr_chiral_restr0.0750.2789
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024801
X-RAY DIFFRACTIONr_nbd_refined0.1860.22637
X-RAY DIFFRACTIONr_nbtor_refined0.3020.24135
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2346
X-RAY DIFFRACTIONr_metal_ion_refined0.1650.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2430.2114
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1430.226
X-RAY DIFFRACTIONr_mcbond_it1.84.43079
X-RAY DIFFRACTIONr_mcangle_it3.1896.5913837
X-RAY DIFFRACTIONr_scbond_it1.9314.513110
X-RAY DIFFRACTIONr_scangle_it3.2436.684539
X-RAY DIFFRACTIONr_lrange_it6.4258.6059089
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.4110.2461250.2562215X-RAY DIFFRACTION96.7742
2.411-2.4770.2831010.2652088X-RAY DIFFRACTION95.4645
2.477-2.5490.312950.2511781X-RAY DIFFRACTION82.9721
2.549-2.6270.252920.2331691X-RAY DIFFRACTION82.8532
2.627-2.7130.2391000.2281919X-RAY DIFFRACTION95.8234
2.713-2.8090.26780.2291988X-RAY DIFFRACTION99.5183
2.809-2.9150.2411000.2171830X-RAY DIFFRACTION99.6901
2.915-3.0330.269940.2121834X-RAY DIFFRACTION99.177
3.033-3.1680.234880.2051710X-RAY DIFFRACTION99.4469
3.168-3.3230.206720.1981674X-RAY DIFFRACTION99.4872
3.323-3.5020.208760.1861584X-RAY DIFFRACTION99.2823
3.502-3.7150.19740.171495X-RAY DIFFRACTION99.3667
3.715-3.9710.171650.1781385X-RAY DIFFRACTION99.2471
3.971-4.2880.236710.1831300X-RAY DIFFRACTION98.6331
4.288-4.6970.174390.171230X-RAY DIFFRACTION99.1406
4.697-5.250.195850.1621057X-RAY DIFFRACTION98.8745
5.25-6.060.206610.21959X-RAY DIFFRACTION99.6094
6.06-7.4170.188430.203827X-RAY DIFFRACTION99.0888
7.417-10.4660.202370.19635X-RAY DIFFRACTION99.4083

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