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- PDB-8wzn: ParkinK211N in complex with phospho NEDD8 -

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Basic information

Entry
Database: PDB / ID: 8wzn
TitleParkinK211N 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 / 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 / RBR-type E3 ubiquitin transferase / regulation of synaptic vesicle transport / positive regulation of mitophagy / 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 / positive regulation of dendrite extension / regulation of dopamine metabolic process / negative regulation of excitatory postsynaptic potential / protein K6-linked ubiquitination / dopaminergic synapse / norepinephrine metabolic process / autophagy of mitochondrion / positive regulation of type 2 mitophagy / protein localization to mitochondrion / 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 / protein neddylation / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / cellular response to L-glutamate / 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 / TGF-beta receptor signaling activates SMADs / cullin family protein binding / negative regulation of reactive oxygen species metabolic process / regulation of glucose metabolic process / regulation of proteolysis / regulation of postsynapse assembly / protein K63-linked ubiquitination / protein deubiquitination / anatomical structure morphogenesis / regulation of synaptic vesicle endocytosis / regulation of protein ubiquitination / protein monoubiquitination / negative regulation of mitochondrial fission / cellular response to unfolded protein / ubiquitin ligase complex / positive regulation of insulin secretion involved in cellular response to glucose stimulus / regulation of postsynaptic membrane neurotransmitter receptor levels / protein K48-linked ubiquitination / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / proteasomal protein catabolic process / phospholipase binding / mitophagy / protein autoubiquitination / negative regulation of reactive oxygen species biosynthetic process / Josephin domain DUBs / ERAD pathway / heat shock protein 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 / 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-like protein NEDD8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 16, 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)46,00613
Polymers45,1652
Non-polymers84211
Water5,747319
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-23 kcal/mol
Surface area19850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.249, 74.603, 80.067
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein E3 ubiquitin-protein ligase parkin


Mass: 36423.535 Da / Num. of mol.: 1 / Mutation: K211N
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-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 319 / 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 Å3/Da / Density % sol: 38.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 0.1 M, MMT, 7.0, 25% w/v, PEG 1500

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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: 1.8→39.86 Å / Num. obs: 32755 / % possible obs: 99.17 % / Redundancy: 4.5 % / CC1/2: 0.996 / Net I/σ(I): 10.25
Reflection shellResolution: 1.8→1.864 Å / Num. unique obs: 3236 / CC1/2: 0.826

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Processing

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

8ikv


Resolution: 1.8→39.86 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.203 / WRfactor Rwork: 0.173 / SU B: 2.9 / SU ML: 0.089 / Average fsc free: 0.9321 / Average fsc work: 0.9415 / Cross valid method: FREE R-VALUE / ESU R: 0.144 / ESU R Free: 0.128
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2116 1753 5.352 %
Rwork0.1788 31002 -
all0.181 --
obs-32755 99.188 %
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: 22.367 Å2
Baniso -1Baniso -2Baniso -3
1--0.169 Å20 Å2-0 Å2
2---0.357 Å20 Å2
3---0.526 Å2
Refinement stepCycle: LAST / Resolution: 1.8→39.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2991 0 29 319 3339
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0123140
X-RAY DIFFRACTIONr_angle_refined_deg1.4791.6654245
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4925392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.24722.284162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.8115530
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8161522
X-RAY DIFFRACTIONr_chiral_restr0.0950.2397
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022389
X-RAY DIFFRACTIONr_nbd_refined0.2020.21402
X-RAY DIFFRACTIONr_nbtor_refined0.3110.22086
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2273
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1910.295
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2030.237
X-RAY DIFFRACTIONr_mcbond_it1.3491.9611541
X-RAY DIFFRACTIONr_mcangle_it2.0922.9321924
X-RAY DIFFRACTIONr_scbond_it2.2122.2491599
X-RAY DIFFRACTIONr_scangle_it3.4773.2522315
X-RAY DIFFRACTIONr_lrange_it7.59727.7754755
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
1.8-1.8470.2651160.22322580.22523910.8940.90699.2890.216
1.847-1.8970.2771150.21422380.21723600.8830.91399.70340.204
1.897-1.9520.231110.21221680.21322800.9070.91599.95610.202
1.952-2.0120.2561180.19621010.19922210.910.92399.910.187
2.012-2.0780.2231130.19620290.19821470.9240.92999.76710.186
2.078-2.1510.221320.18719560.18920900.9310.94299.90430.178
2.151-2.2320.23970.17218810.17520050.9370.95398.65340.163
2.232-2.3240.2351060.17118390.17419500.9340.95599.74360.163
2.324-2.4270.2241070.17717670.1818780.9470.9599.7870.167
2.427-2.5450.211960.18816760.18917750.9430.94399.8310.178
2.545-2.6830.233920.17615880.17916870.9330.95199.58510.167
2.683-2.8450.208730.1815210.18216070.9480.95599.1910.172
2.845-3.0410.221870.19214380.19415390.950.95299.09030.185
3.041-3.2850.212720.17913430.18114200.9490.95499.64790.174
3.285-3.5980.22770.16512240.16813110.9510.96299.23720.163
3.598-4.0210.161630.15611270.15712100.970.96998.34710.157
4.021-4.6410.163510.159880.15110630.9670.96997.74220.153
4.641-5.680.178650.1628280.1639180.9680.9797.27670.166
5.68-8.0120.224430.1926580.1947320.9440.96495.7650.193
8.012-80.0670.181190.1653740.1664390.970.97489.52160.176

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