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- PDB-5c9v: Structure of human Parkin G319A -

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Basic information

Entry
Database: PDB / ID: 5c9v
TitleStructure of human Parkin G319A
ComponentsE3 ubiquitin-protein ligase parkin
KeywordsSIGNALING PROTEIN / Parkin / ubiquitin / E3 ligase / RBR / Parkinson's disease / mitophagy / cell signalling
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 / negative regulation of spontaneous neurotransmitter secretion / regulation of protein targeting to mitochondrion / 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 / negative regulation of spontaneous neurotransmitter secretion / regulation of protein targeting to mitochondrion / negative regulation of intralumenal vesicle formation / negative regulation of glucokinase activity / mitochondrion to lysosome vesicle-mediated transport / negative regulation of exosomal secretion / parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization / Lewy body / protein K27-linked ubiquitination / Parkin-FBXW7-Cul1 ubiquitin ligase complex / positive regulation of mitochondrial fusion / regulation of synaptic vesicle transport / negative regulation of actin filament bundle assembly / free ubiquitin chain polymerization / protein K29-linked ubiquitination / 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 / cellular response to toxic substance / positive regulation of mitophagy / regulation of necroptotic process / regulation of cellular response to oxidative stress / autophagy of mitochondrion / regulation of dopamine metabolic process / dopaminergic synapse / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of dendrite extension / protein K6-linked ubiquitination / norepinephrine metabolic process / positive regulation of proteasomal protein catabolic 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 / cellular response to dopamine / 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 / regulation of canonical Wnt signaling pathway / aggresome / regulation of reactive oxygen species metabolic process / regulation of synaptic vesicle endocytosis / dopamine uptake involved in synaptic transmission / dopamine metabolic process / positive regulation of DNA binding / positive regulation of mitochondrial fission / regulation of dopamine secretion / ubiquitin-specific protease binding / negative regulation of release of cytochrome c from mitochondria / startle response / protein monoubiquitination / cullin family protein binding / phospholipase binding / protein K63-linked ubiquitination / regulation of protein ubiquitination / mitophagy / regulation of glucose metabolic process / negative regulation of reactive oxygen species metabolic process / cellular response to unfolded protein / proteasomal protein catabolic process / cellular response to manganese ion / negative regulation of insulin secretion / protein K48-linked ubiquitination / protein autoubiquitination / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / ERAD pathway / ubiquitin ligase complex / heat shock protein binding / Hsp70 protein binding / PINK1-PRKN Mediated Mitophagy / tubulin binding / response to endoplasmic reticulum stress / adult locomotory behavior / Josephin domain DUBs / negative regulation of protein phosphorylation / regulation of mitochondrial membrane potential / mitochondrion organization / learning / ubiquitin binding / regulation of autophagy / synaptic transmission, glutamatergic / central nervous system development / G protein-coupled receptor binding / PDZ domain binding / macroautophagy / protein destabilization / regulation of protein stability / negative regulation of canonical Wnt signaling pathway
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 family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
E3 ubiquitin-protein ligase parkin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsWauer, T. / Komander, D.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)U105192732 United Kingdom
European Research Council309756 United Kingdom
Citation
Journal: Nature / Year: 2015
Title: Mechanism of phospho-ubiquitin-induced PARKIN activation.
Authors: Wauer, T. / Simicek, M. / Schubert, A. / Komander, D.
#1: Journal: EMBO J. / Year: 2013
Title: Structure of the human Parkin ligase domain in an autoinhibited state.
Authors: Wauer, T. / Komander, D.
History
DepositionJun 29, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2015Group: Database references
Revision 1.2Aug 26, 2015Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 10, 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

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase parkin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,26818
Polymers36,8921
Non-polymers1,37617
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-58 kcal/mol
Surface area16870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.360, 169.360, 96.990
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-510-

SO4

21A-601-

HOH

31A-632-

HOH

41A-680-

HOH

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Components

#1: Protein E3 ubiquitin-protein ligase parkin / Parkin / Parkinson juvenile disease protein 2 / Parkinson disease protein 2


Mass: 36892.129 Da / Num. of mol.: 1 / Fragment: UNP residues 137-465 / Mutation: G319A
Source method: isolated from a genetically manipulated source
Details: engineered mutation at position G319A / Source: (gene. exp.) Homo sapiens (human) / Gene: PARK2, PRKN / Plasmid: pOPINK
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O60260, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.63 Å3/Da / Density % sol: 66.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 1.8 M lithium sulphate, 0.01 M MgCl2, 0.05 M MES pH 5.6
PH range: 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.35→86.68 Å / Num. obs: 22270 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Biso Wilson estimate: 42.5 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 13.3
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4bm9

4bm9


Resolution: 2.35→84.68 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2287 1148 5.15 %random selection
Rwork0.1983 ---
obs0.1998 22270 99.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.3 Å2
Refinement stepCycle: LAST / Resolution: 2.35→84.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2349 0 56 81 2486
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032450
X-RAY DIFFRACTIONf_angle_d0.6913324
X-RAY DIFFRACTIONf_dihedral_angle_d13.913872
X-RAY DIFFRACTIONf_chiral_restr0.029346
X-RAY DIFFRACTIONf_plane_restr0.003432
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.4570.28521520.27222598X-RAY DIFFRACTION100
2.457-2.58650.31191580.26242590X-RAY DIFFRACTION100
2.5865-2.74860.28081370.25282638X-RAY DIFFRACTION100
2.7486-2.96080.2631320.25222641X-RAY DIFFRACTION100
2.9608-3.25880.22111480.22822634X-RAY DIFFRACTION100
3.2588-3.73040.21671470.19812616X-RAY DIFFRACTION100
3.7304-4.69980.22671310.15852681X-RAY DIFFRACTION100
4.6998-84.7350.19041430.17012724X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 7.8845 Å / Origin y: 31.4194 Å / Origin z: 36.9402 Å
111213212223313233
T0.3663 Å2-0.014 Å20.0139 Å2-0.3066 Å20.0305 Å2--0.2457 Å2
L4.1353 °21.1426 °20.0605 °2-1.2053 °2-0.1762 °2--0.6839 °2
S-0.0275 Å °0.2777 Å °-0.0836 Å °0.0212 Å °0.0596 Å °-0.0111 Å °-0.0069 Å °0.0155 Å °-0.0337 Å °
Refinement TLS groupSelection details: chain A

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