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- PDB-8wzo: Parkin in complex with phospho NEDD8 -

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Basic information

Entry
Database: PDB / ID: 8wzo
TitleParkin in complex with phospho NEDD8
Components
  • E3 ubiquitin-protein ligase parkin
  • NEDD8
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 / 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 / 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 / protein neddylation / 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 / TGF-beta receptor signaling activates SMADs / cullin family protein binding / negative regulation of reactive oxygen species metabolic process / regulation of postsynapse assembly / regulation of glucose metabolic process / regulation of proteolysis / protein K63-linked ubiquitination / protein deubiquitination / anatomical structure morphogenesis / protein monoubiquitination / regulation of protein ubiquitination / cellular response to manganese ion / ubiquitin ligase complex / cellular response to unfolded protein / negative regulation of insulin secretion / proteasomal protein catabolic process / protein K48-linked ubiquitination / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / mitophagy / protein autoubiquitination / ERAD pathway / heat shock protein binding / Hsp70 protein binding / tubulin binding / response to endoplasmic reticulum stress / regulation of mitochondrial membrane potential / adult locomotory behavior / Josephin domain DUBs / central nervous system development / ubiquitin binding / learning / PINK1-PRKN Mediated Mitophagy / synaptic transmission, glutamatergic / PDZ domain binding / mitochondrion organization / macroautophagy / G protein-coupled receptor binding
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 / Nedd8-like ubiquitin / : / 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
E3 ubiquitin-protein ligase parkin / Ubiquitin-like protein NEDD8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsLenka, D.R. / Kumar, A.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India) India
CitationJournal: Structure
Title: Parkin in complex with phospho NEDD8
Authors: Lenka, D.R. / Kumar, A.
History
DepositionNov 2, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 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
A: E3 ubiquitin-protein ligase parkin
B: NEDD8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,88913
Polymers45,1802
Non-polymers70911
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-45 kcal/mol
Surface area18690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.976, 47.747, 127.859
Angle α, β, γ (deg.)90.000, 105.380, 90.000
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-647-

HOH

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Components

#1: Protein E3 ubiquitin-protein ligase parkin


Mass: 36438.613 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKN / Production host: Escherichia coli (E. coli) / References: UniProt: O60260
#2: Protein NEDD8


Mass: 8741.034 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NEDD8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15843
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.54 Å3/Da / Density % sol: 51.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 0.02 M Sodium/potassium phosphate, 0.1 M Bis-Tris propane, 7.5, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.8731 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 2.25→44.52 Å / Num. obs: 21772 / % possible obs: 99.8 % / Redundancy: 4.3 % / CC1/2: 0.993 / Net I/σ(I): 8.4
Reflection shellResolution: 2.25→2.32 Å / Num. unique obs: 1974 / CC1/2: 0.643

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N2W

5n2w


Resolution: 2.25→40.947 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.923 / WRfactor Rfree: 0.242 / WRfactor Rwork: 0.201 / SU B: 7.117 / SU ML: 0.173 / Average fsc free: 0.8838 / Average fsc work: 0.9042 / Cross valid method: FREE R-VALUE / ESU R: 0.294 / ESU R Free: 0.221
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2485 1097 5.039 %
Rwork0.2072 20672 -
all0.209 --
obs-21769 99.689 %
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: 45.106 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å2-0 Å2-1.342 Å2
2---0.216 Å2-0 Å2
3---1.133 Å2
Refinement stepCycle: LAST / Resolution: 2.25→40.947 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2929 0 20 174 3123
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0123035
X-RAY DIFFRACTIONr_angle_refined_deg1.0261.6674098
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6455374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.2622.038157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.86815495
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7731521
X-RAY DIFFRACTIONr_chiral_restr0.0780.2383
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022321
X-RAY DIFFRACTIONr_nbd_refined0.1840.21205
X-RAY DIFFRACTIONr_nbtor_refined0.2990.22017
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2179
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1790.239
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1210.29
X-RAY DIFFRACTIONr_mcbond_it1.6164.5161508
X-RAY DIFFRACTIONr_mcangle_it2.8586.7571878
X-RAY DIFFRACTIONr_scbond_it1.7744.5771527
X-RAY DIFFRACTIONr_scangle_it2.896.8012220
X-RAY DIFFRACTIONr_lrange_it6.37359.3314344
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.25-2.3090.321710.27415130.27615840.7650.8091000.272
2.309-2.3720.299790.26414870.26615690.820.85599.80880.261
2.372-2.440.237730.25414170.25314950.8760.86799.66560.248
2.44-2.5150.328870.25314030.25714910.8150.86399.93290.245
2.515-2.5980.283750.24213360.24414130.8580.88799.85850.231
2.598-2.6890.31530.23413560.23714110.860.89899.85830.222
2.689-2.790.301640.22412850.22713520.8840.91499.77810.209
2.79-2.9040.245790.22311900.22512720.9140.90799.76420.208
2.904-3.0330.271560.2211680.22212260.8950.9199.83690.204
3.033-3.1810.274730.21211090.21511850.8920.92599.74680.195
3.181-3.3520.256590.21810540.2211170.9040.92499.64190.208
3.352-3.5550.211520.19910110.210690.9420.94399.43870.192
3.555-3.80.266450.199510.19310030.9210.94899.30210.184
3.8-4.1040.215610.1918920.1939550.9490.94699.79060.187
4.104-4.4940.223370.1758020.1778420.9540.95899.64370.179
4.494-5.0220.222300.1797680.188000.9370.95699.750.185
5.022-5.7940.226410.1866630.1897040.9380.9541000.196
5.794-7.0860.329260.2115720.2166000.9060.94299.66670.219
7.086-9.9740.157220.1754480.1744720.9520.95799.57630.188
9.974-73.4260.176140.1662470.1672760.9790.96894.56520.183

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