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- PDB-8ikt: Ternary trans-complex of phospho-parkin with cis ACT and pUb -

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Basic information

Entry
Database: PDB / ID: 8ikt
TitleTernary trans-complex of phospho-parkin with cis ACT and pUb
Components
  • (E3 ubiquitin-protein ligase ...) x 2
  • Ubiquitin
KeywordsLIGASE / 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
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 / E3 ubiquitin ligase RBR family ...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 / E3 ubiquitin ligase RBR family / 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
3-AMINOPROPANE / 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: 2.6 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 / Derived calculations / Category: citation / citation_author / struct_conn / Item: _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)52,31313
Polymers51,5593
Non-polymers75410
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-39 kcal/mol
Surface area17270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.764, 82.764, 103.494
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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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: 34043.469 Da / Num. of mol.: 1 / Mutation: Q347C
Source method: isolated from a genetically manipulated source
Details: LTRVDL corresponds to the 102 to 107 region of the protein. The mismatch in the alignment is due to the missing electron density of the region in between.
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: 8916.063 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 , 5 types, 62 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.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#7: Chemical ChemComp-3CN / 3-AMINOPROPANE


Mass: 59.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9N / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.98 Å3/Da / Density % sol: 38.02 %
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, Imidazole, MES monohydrate (acid), 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: BM07 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 22, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→38.42 Å / Num. obs: 13050 / % possible obs: 99.9 % / Redundancy: 13.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.144 / Net I/σ(I): 17.1
Reflection shellResolution: 2.6→2.72 Å / Num. unique obs: 1558 / CC1/2: 0.791

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8IKM

8ikm


Resolution: 2.6→38.42 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.932 / SU B: 32.393 / SU ML: 0.288 / Cross valid method: FREE R-VALUE / ESU R Free: 0.313
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2358 691 5.306 %
Rwork0.2125 12333 -
all0.214 --
obs-12333 99.87 %
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: 63.575 Å2
Baniso -1Baniso -2Baniso -3
1--1.814 Å2-0.907 Å2-0 Å2
2---1.814 Å2-0 Å2
3---5.883 Å2
Refinement stepCycle: LAST / Resolution: 2.6→38.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2977 0 30 52 3059
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0123117
X-RAY DIFFRACTIONr_angle_refined_deg0.8441.6564223
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8875395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.85722.581155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.86315508
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.9931519
X-RAY DIFFRACTIONr_chiral_restr0.0630.2411
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022335
X-RAY DIFFRACTIONr_nbd_refined0.1980.21531
X-RAY DIFFRACTIONr_nbtor_refined0.3030.22127
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2167
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1880.247
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1590.213
X-RAY DIFFRACTIONr_mcbond_it1.8366.4431552
X-RAY DIFFRACTIONr_mcangle_it2.9459.6471935
X-RAY DIFFRACTIONr_scbond_it1.8416.4791563
X-RAY DIFFRACTIONr_scangle_it2.7299.6542279
X-RAY DIFFRACTIONr_lrange_it5.68788.0214720
X-RAY DIFFRACTIONr_rigid_bond_restr0.23733115
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.6680.307550.302888X-RAY DIFFRACTION100
2.668-2.7410.335470.286875X-RAY DIFFRACTION100
2.741-2.820.307670.266831X-RAY DIFFRACTION100
2.907-3.0020.306520.244825X-RAY DIFFRACTION100
3.002-3.1070.275380.256772X-RAY DIFFRACTION100
3.107-3.2250.258490.234741X-RAY DIFFRACTION100
3.225-3.3560.296510.245714X-RAY DIFFRACTION100
3.356-3.5050.27480.212680X-RAY DIFFRACTION100
3.505-3.6760.249300.197692X-RAY DIFFRACTION100
4.109-4.3930.199320.181569X-RAY DIFFRACTION99.0115
4.744-5.1950.224240.178499X-RAY DIFFRACTION100
5.195-5.8070.236210.213444X-RAY DIFFRACTION99.7854
5.807-6.7020.27240.205410X-RAY DIFFRACTION100
6.702-8.1990.219170.175345X-RAY DIFFRACTION100

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