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- PDB-8w31: Crystal structure of parkin (R0RB):2pUb with activator compound -

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Basic information

Entry
Database: PDB / ID: 8w31
TitleCrystal structure of parkin (R0RB):2pUb with activator compound
Components
  • E3 ubiquitin-protein ligase parkin
  • Ubiquitin
KeywordsLIGASE / E3-ubiquitin ligase / activator
Function / homology
Function and homology information


Josephin domain DUBs / Regulation of necroptotic cell death / Aggrephagy / positive regulation of neurotransmitter uptake / regulation protein catabolic process at presynapse / negative regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway / cellular response to L-glutamine / PINK1-PRKN Mediated Mitophagy / negative regulation of spontaneous neurotransmitter secretion / Antigen processing: Ubiquitination & Proteasome degradation ...Josephin domain DUBs / Regulation of necroptotic cell death / Aggrephagy / positive regulation of neurotransmitter uptake / regulation protein catabolic process at presynapse / negative regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway / cellular response to L-glutamine / PINK1-PRKN Mediated Mitophagy / negative regulation of spontaneous neurotransmitter secretion / Antigen processing: Ubiquitination & Proteasome degradation / negative regulation of intralumenal vesicle formation / negative regulation of glucokinase activity / negative regulation of exosomal secretion / mitochondrion to lysosome vesicle-mediated transport / response to curcumin / cellular response to hydrogen sulfide / parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization / Parkin-FBXW7-Cul1 ubiquitin ligase complex / negative regulation of actin filament bundle assembly / positive regulation of mitochondrial fusion / free ubiquitin chain polymerization / negative regulation of mitochondrial fusion / positive regulation of mitophagy in response to mitochondrial depolarization / positive regulation of protein linear polyubiquitination / F-box domain binding / RBR-type E3 ubiquitin transferase / negative regulation by host of viral genome replication / mitochondrion localization / mitochondrial fragmentation involved in apoptotic process / cellular response to toxic substance / positive regulation of mitophagy / intracellular vesicle / autophagy of mitochondrion / regulation of cellular response to oxidative stress / negative regulation of excitatory postsynaptic potential / regulation of neurotransmitter secretion / regulation of dopamine metabolic process / dopaminergic synapse / cellular response to L-glutamate / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / 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 / protein metabolic process / negative regulation of synaptic transmission, glutamatergic / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / synaptic transmission, dopaminergic / positive regulation of tumor necrosis factor-mediated signaling pathway / mitochondrial fission / protein K11-linked ubiquitination / aggresome assembly / ubiquitin conjugating enzyme binding / regulation of mitochondrion organization / hypothalamus gonadotrophin-releasing hormone neuron development / aggresome / response to muscle activity / positive regulation of mitochondrial membrane potential / female meiosis I / regulation of reactive oxygen species metabolic process / positive regulation of protein monoubiquitination / regulation of synaptic vesicle endocytosis / mitochondrion transport along microtubule / fat pad development / negative regulation of mitochondrial fission / response to corticosterone / dopamine uptake involved in synaptic transmission / positive regulation of DNA binding / dopamine metabolic process / positive regulation of mitochondrial fission / positive regulation of ATP biosynthetic process / female gonad development / seminiferous tubule development / ubiquitin-specific protease binding / negative regulation of release of cytochrome c from mitochondria / male meiosis I / startle response / protein monoubiquitination / positive regulation of insulin secretion involved in cellular response to glucose stimulus / cullin family protein binding / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / regulation of postsynaptic membrane neurotransmitter receptor levels / phospholipase binding / protein K63-linked ubiquitination / regulation of protein ubiquitination / mitophagy / response to unfolded protein / negative regulation of reactive oxygen species metabolic process / cellular response to manganese ion / proteasomal protein catabolic process / negative regulation of insulin secretion / protein K48-linked ubiquitination / protein autoubiquitination / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / neuron projection morphogenesis / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process
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 / 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. / : / 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
: / Polyubiquitin-B / E3 ubiquitin-protein ligase parkin
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSauve, V. / Gehring, K.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)FDN 159903 Canada
CitationJournal: Nat Commun / Year: 2024
Title: Activation of Parkin by a Molecular Glue
Authors: Sauve, V. / Gehring, K.
History
DepositionFeb 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release

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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: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,58111
Polymers43,6063
Non-polymers9758
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-22 kcal/mol
Surface area18720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.540, 83.540, 258.770
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)

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Components

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Protein , 2 types, 3 molecules ABC

#1: Protein E3 ubiquitin-protein ligase parkin / Parkin RBR E3 ubiquitin-protein ligase


Mass: 26406.189 Da / Num. of mol.: 1 / Fragment: residues 145-379
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Prkn, Park2 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9JK66, RBR-type E3 ubiquitin transferase
#2: Protein Ubiquitin


Mass: 8599.758 Da / Num. of mol.: 2 / Fragment: residues 1-75
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0CG47

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Non-polymers , 4 types, 40 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-A1AE9 / (S)-1-(6-benzyl-3-(4-(1,2,3,4-tetrahydroquinoline-1-carbonyl)phenyl)-6,7-dihydropyrazolo[1,5-a]pyrazin-5(4H)-yl)ethan-1-one / 1-[(6S,8R)-6-benzyl-3-[4-(3,4-dihydroquinoline-1(2H)-carbonyl)phenyl]-6,7-dihydropyrazolo[1,5-a]pyrazin-5(4H)-yl]ethan-1-one


Mass: 490.596 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H30N4O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.99 Å3/Da / Density % sol: 58.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M Sodium Chloride, 0.1M HEPES pH 7.5, 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.953 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 19, 2023
RadiationMonochromator: axilon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 2.5→48.22 Å / Num. obs: 19414 / % possible obs: 99.95 % / Redundancy: 38.3 % / Biso Wilson estimate: 76.3 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.018 / Rrim(I) all: 0.112 / Net I/σ(I): 24.08
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 40.7 % / Rmerge(I) obs: 2.938 / Mean I/σ(I) obs: 1.72 / Num. unique obs: 1881 / CC1/2: 0.718 / CC star: 0.914 / Rpim(I) all: 0.464 / Rrim(I) all: 2.98 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
XDSdata scaling
XDSdata reduction
PHENIX1.20.1-4487phasing
Coot0.9.8.91model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→48.22 Å / SU ML: 0.5182 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.9963
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2937 971 5 %
Rwork0.2397 18443 -
obs0.2423 19414 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 89.24 Å2
Refinement stepCycle: LAST / Resolution: 2.5→48.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2970 0 49 32 3051
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01033071
X-RAY DIFFRACTIONf_angle_d1.28094153
X-RAY DIFFRACTIONf_chiral_restr0.0699456
X-RAY DIFFRACTIONf_plane_restr0.0097555
X-RAY DIFFRACTIONf_dihedral_angle_d18.16381188
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.630.44311350.40072561X-RAY DIFFRACTION100
2.63-2.80.45991340.34822563X-RAY DIFFRACTION100
2.8-3.010.41421360.3412578X-RAY DIFFRACTION100
3.01-3.320.38521360.33132587X-RAY DIFFRACTION100
3.32-3.790.3431390.27312628X-RAY DIFFRACTION100
3.8-4.780.24981400.20952658X-RAY DIFFRACTION100
4.78-48.220.24111510.19262868X-RAY DIFFRACTION99.87

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