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- PDB-6hue: ParkinS65N -

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Basic information

Entry
Database: PDB / ID: 6hue
TitleParkinS65N
ComponentsE3 ubiquitin-protein ligase parkin
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 / 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 / cellular response to L-glutamine / : / negative regulation of exosomal secretion / mitochondrion to lysosome vesicle-mediated transport / type 2 mitophagy / negative regulation of glucokinase activity / response to curcumin / negative regulation of mitochondrial fusion / cellular response to hydrogen sulfide / protein K29-linked ubiquitination / free ubiquitin chain polymerization / Lewy body / positive regulation of protein linear polyubiquitination / host-mediated suppression of viral genome replication / RBR-type E3 ubiquitin transferase / Parkin-FBXW7-Cul1 ubiquitin ligase complex / regulation of synaptic vesicle transport / positive regulation of mitochondrial fusion / negative regulation of actin filament bundle assembly / positive regulation of mitophagy / F-box domain binding / regulation of necroptotic process / mitochondrial fragmentation involved in apoptotic process / regulation of cellular response to oxidative stress / positive regulation of dendrite extension / regulation of dopamine metabolic process / negative regulation of excitatory postsynaptic potential / protein K6-linked ubiquitination / norepinephrine metabolic process / dopaminergic synapse / autophagy of mitochondrion / positive regulation of type 2 mitophagy / mitochondrion localization / protein localization to mitochondrion / positive regulation of tumor necrosis factor-mediated signaling pathway / cellular response to dopamine / positive regulation of proteasomal protein catabolic process / positive regulation of protein localization to membrane / mitochondrial fission / cellular response to toxic substance / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / protein K27-linked ubiquitination / aggresome assembly / cellular response to L-glutamate / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / protein K11-linked ubiquitination / regulation of mitochondrion organization / regulation of canonical Wnt signaling pathway / ubiquitin conjugating enzyme binding / negative regulation of synaptic transmission, glutamatergic / positive regulation of mitochondrial membrane potential / negative regulation of JNK cascade / aggresome / regulation of reactive oxygen species metabolic process / positive regulation of mitochondrial fission / response to corticosterone / response to muscle activity / negative regulation of release of cytochrome c from mitochondria / ubiquitin-specific protease binding / startle response / dopamine uptake involved in synaptic transmission / dopamine metabolic process / regulation of dopamine secretion / positive regulation of ATP biosynthetic process / negative regulation of reactive oxygen species metabolic process / regulation of glucose metabolic process / cullin family protein binding / regulation of protein ubiquitination / protein deubiquitination / cellular response to unfolded protein / protein K63-linked ubiquitination / regulation of synaptic vesicle endocytosis / protein monoubiquitination / negative regulation of mitochondrial fission / ubiquitin ligase complex / positive regulation of insulin secretion involved in cellular response to glucose stimulus / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / regulation of postsynaptic membrane neurotransmitter receptor levels / protein autoubiquitination / protein K48-linked ubiquitination / mitophagy / phospholipase binding / proteasomal protein catabolic process / negative regulation of reactive oxygen species biosynthetic process / cellular response to manganese ion / heat shock protein binding / ERAD pathway / Hsp70 protein binding / tubulin binding / response to endoplasmic reticulum stress / ubiquitin binding / central nervous system development
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. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase parkin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsMcWilliams, T.G. / Barini, E. / Pohjolan-Pirhonen, R. / Brooks, S.P. / Singh, F. / Burel, S. / Balk, K. / Kumar, A. / Montava-Garriga, L. / Prescott, A.R. ...McWilliams, T.G. / Barini, E. / Pohjolan-Pirhonen, R. / Brooks, S.P. / Singh, F. / Burel, S. / Balk, K. / Kumar, A. / Montava-Garriga, L. / Prescott, A.R. / Hassoun, S.M. / Mouton-Liger, F. / Ball, G. / Hills, R. / Knebel, A. / Ulusoy, A. / Di Monte, D.A. / Tamjar, J. / Antico, O. / Fears, K. / Smith, L. / Brambilla, R. / Palin, E. / Valori, M. / Eerola-Rautio, J. / Tienari, P. / Corti, O. / Dunnett, S.B. / Ganley, I.G. / Suomalainen, A. / Muqit, M.M.K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust101022/Z/13/Z United Kingdom
CitationJournal: Open Biology / Year: 2018
Title: Phosphorylation of Parkin at serine 65 is essential for its activation in vivo .
Authors: McWilliams, T.G. / Barini, E. / Pohjolan-Pirhonen, R. / Brooks, S.P. / Singh, F. / Burel, S. / Balk, K. / Kumar, A. / Montava-Garriga, L. / Prescott, A.R. / Hassoun, S.M. / Mouton-Liger, F. ...Authors: McWilliams, T.G. / Barini, E. / Pohjolan-Pirhonen, R. / Brooks, S.P. / Singh, F. / Burel, S. / Balk, K. / Kumar, A. / Montava-Garriga, L. / Prescott, A.R. / Hassoun, S.M. / Mouton-Liger, F. / Ball, G. / Hills, R. / Knebel, A. / Ulusoy, A. / Di Monte, D.A. / Tamjar, J. / Antico, O. / Fears, K. / Smith, L. / Brambilla, R. / Palin, E. / Valori, M. / Eerola-Rautio, J. / Tienari, P. / Corti, O. / Dunnett, S.B. / Ganley, I.G. / Suomalainen, A. / Muqit, M.M.K.
History
DepositionOct 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Sep 30, 2020Group: Database references / Category: citation / Item: _citation.journal_abbrev / _citation.title
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: E3 ubiquitin-protein ligase parkin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,98226
Polymers91,3042
Non-polymers1,67824
Water2,828157
1
A: E3 ubiquitin-protein ligase parkin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,49113
Polymers45,6521
Non-polymers83912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: E3 ubiquitin-protein ligase parkin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,49113
Polymers45,6521
Non-polymers83912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.431, 66.870, 206.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#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: 45652.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKN, PARK2 / Production host: Escherichia coli (E. coli)
References: UniProt: O60260, RBR-type E3 ubiquitin transferase

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Non-polymers , 5 types, 181 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O

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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: 2.51 Å3/Da / Density % sol: 51.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 100mM BIS-TRIS pH 5.5, 200mM LiSO4 and 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.85→47.98 Å / Num. obs: 21291 / % possible obs: 96.1 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 4.5
Reflection shellResolution: 2.85→2.95 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C1Z

5c1z


Resolution: 2.85→47.98 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.913 / SU B: 24.598 / SU ML: 0.407 / Cross valid method: THROUGHOUT / ESU R Free: 0.422 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25486 1095 5.2 %RANDOM
Rwork0.22284 ---
obs0.22449 20094 95.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 64.964 Å2
Baniso -1Baniso -2Baniso -3
1-1.58 Å20 Å20 Å2
2--4.08 Å20 Å2
3----5.66 Å2
Refinement stepCycle: 1 / Resolution: 2.85→47.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5992 0 52 159 6203
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196380
X-RAY DIFFRACTIONr_bond_other_d0.0020.025847
X-RAY DIFFRACTIONr_angle_refined_deg1.5791.9448645
X-RAY DIFFRACTIONr_angle_other_deg1.0373.00813399
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8385792
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.86323.481316
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.971151040
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5311556
X-RAY DIFFRACTIONr_chiral_restr0.0840.2913
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217257
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021551
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.9076.4633084
X-RAY DIFFRACTIONr_mcbond_other3.9076.4633083
X-RAY DIFFRACTIONr_mcangle_it6.2739.6673847
X-RAY DIFFRACTIONr_mcangle_other6.2729.6673848
X-RAY DIFFRACTIONr_scbond_it3.6836.6683296
X-RAY DIFFRACTIONr_scbond_other3.6836.6683296
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0319.8984780
X-RAY DIFFRACTIONr_long_range_B_refined11.33759.66925053
X-RAY DIFFRACTIONr_long_range_B_other11.33259.68325028
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.85→2.924 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 69 -
Rwork0.369 1425 -
obs--91.88 %

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