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- PDB-5c23: Parkin (S65DUblR0RBR) -

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Basic information

Entry
Database: PDB / ID: 5c23
TitleParkin (S65DUblR0RBR)
ComponentsE3 ubiquitin-protein ligase parkin
KeywordsLIGASE / E3 ligase2
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 / : / 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 / 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 / positive regulation of protein linear polyubiquitination / RBR-type E3 ubiquitin transferase / host-mediated suppression of viral genome replication / regulation of synaptic vesicle transport / Parkin-FBXW7-Cul1 ubiquitin ligase complex / positive regulation of mitochondrial fusion / negative regulation of actin filament bundle assembly / regulation of necroptotic process / positive regulation of mitophagy / mitochondrial fragmentation involved in apoptotic process / F-box domain binding / regulation of cellular response to oxidative stress / positive regulation of dendrite extension / regulation of dopamine metabolic process / negative regulation of excitatory postsynaptic potential / norepinephrine metabolic process / autophagy of mitochondrion / positive regulation of type 2 mitophagy / dopaminergic synapse / mitochondrion localization / protein localization to mitochondrion / cellular response to dopamine / mitochondrial fission / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of protein localization to membrane / cellular response to toxic substance / positive regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / regulation of mitochondrion organization / protein K11-linked ubiquitination / aggresome assembly / cellular response to L-glutamate / positive regulation of proteasomal protein catabolic process / protein K6-linked ubiquitination / ubiquitin conjugating enzyme binding / regulation of canonical Wnt signaling pathway / aggresome / negative regulation of synaptic transmission, glutamatergic / negative regulation of JNK cascade / protein K27-linked ubiquitination / positive regulation of mitochondrial membrane potential / regulation of reactive oxygen species metabolic process / positive regulation of mitochondrial fission / response to muscle activity / negative regulation of release of cytochrome c from mitochondria / response to corticosterone / Lewy body / ubiquitin-specific protease binding / startle response / dopamine metabolic process / dopamine uptake involved in synaptic transmission / regulation of dopamine secretion / negative regulation of reactive oxygen species metabolic process / regulation of glucose metabolic process / positive regulation of ATP biosynthetic process / regulation of protein ubiquitination / cellular response to unfolded protein / cullin family protein binding / regulation of synaptic vesicle endocytosis / protein deubiquitination / negative regulation of mitochondrial fission / protein monoubiquitination / ubiquitin ligase complex / protein K63-linked ubiquitination / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / regulation of postsynaptic membrane neurotransmitter receptor levels / protein autoubiquitination / mitophagy / phospholipase binding / negative regulation of reactive oxygen species biosynthetic process / cellular response to manganese ion / ERAD pathway / heat shock protein binding / protein K48-linked ubiquitination / proteasomal protein catabolic process / Hsp70 protein binding / response to endoplasmic reticulum stress / positive regulation of insulin secretion involved in cellular response to glucose stimulus / central nervous system development / regulation of autophagy / Josephin domain DUBs / PINK1-PRKN Mediated Mitophagy
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: 2.37 Å
AuthorsKumar, A. / Aguirre, J.D. / Condos, T.E.C. / Martinez-Torres, R.J. / Chaugule, V.K. / Toth, R. / Sundaramoorthy, R. / Mercier, P. / Knebel, A. / Spratt, D.E. ...Kumar, A. / Aguirre, J.D. / Condos, T.E.C. / Martinez-Torres, R.J. / Chaugule, V.K. / Toth, R. / Sundaramoorthy, R. / Mercier, P. / Knebel, A. / Spratt, D.E. / Barber, K.R. / Shaw, G.S. / Walden, H.
CitationJournal: Embo J. / Year: 2015
Title: Disruption of the autoinhibited state primes the E3 ligase parkin for activation and catalysis.
Authors: Kumar, A. / Aguirre, J.D. / Condos, T.E. / Martinez-Torres, R.J. / Chaugule, V.K. / Toth, R. / Sundaramoorthy, R. / Mercier, P. / Knebel, A. / Spratt, D.E. / Barber, K.R. / Shaw, G.S. / Walden, H.
History
DepositionJun 15, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Database references
Revision 1.2Oct 28, 2015Group: Database references
Revision 1.3Jan 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
B: E3 ubiquitin-protein ligase parkin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,04526
Polymers91,3062
Non-polymers1,73924
Water5,639313
1
A: E3 ubiquitin-protein ligase parkin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,58814
Polymers45,6531
Non-polymers93513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: E3 ubiquitin-protein ligase parkin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,45712
Polymers45,6531
Non-polymers80411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.279, 66.290, 205.639
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 / Parkinson juvenile disease protein 2 / Parkinson disease protein 2


Mass: 45653.023 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARK2, PRKN / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O60260, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)

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Non-polymers , 5 types, 337 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 2.47 Å3/Da / Density % sol: 50.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 5.5 / Details: PEG3350, LiSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9172 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9172 Å / Relative weight: 1
ReflectionResolution: 2.37→23.16 Å / Num. all: 37544 / Num. obs: 35690 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 45.97 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 7.7
Reflection shellResolution: 2.37→2.46 Å / Redundancy: 5 % / Rmerge(I) obs: 1.17 / % possible all: 98.8

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
iMOSFLMdata reduction
SCALAdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C1Z

5c1z


Resolution: 2.37→23.16 Å / Cor.coef. Fo:Fc: 0.9122 / Cor.coef. Fo:Fc free: 0.9052 / SU R Cruickshank DPI: 0.381 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.413 / SU Rfree Blow DPI: 0.238 / SU Rfree Cruickshank DPI: 0.234
RfactorNum. reflection% reflectionSelection details
Rfree0.2406 1854 4.94 %RANDOM
Rwork0.2199 ---
obs0.2209 37544 99.79 %-
Displacement parametersBiso mean: 52.88 Å2
Baniso -1Baniso -2Baniso -3
1--5.2013 Å20 Å20 Å2
2---6.8496 Å20 Å2
3---12.051 Å2
Refine analyzeLuzzati coordinate error obs: 0.376 Å
Refinement stepCycle: 1 / Resolution: 2.37→23.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6055 0 56 313 6424
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0076236HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.878450HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2138SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes162HARMONIC2
X-RAY DIFFRACTIONt_gen_planes910HARMONIC5
X-RAY DIFFRACTIONt_it6236HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.74
X-RAY DIFFRACTIONt_other_torsion19.01
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion782SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6857SEMIHARMONIC4
LS refinement shellResolution: 2.37→2.44 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.2672 145 5.23 %
Rwork0.2406 2625 -
all0.2419 2770 -
obs--99.79 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.986-0.4733-1.00381.16650.9371.8479-0.03610.0512-0.002-0.0124-0.02070.040.0714-0.16330.0568-0.1016-0.0187-0.0068-0.13110.0064-0.2264-6.35962.997843.1001
21.1729-0.50520.98111.0031-0.97791.9459-0.0445-0.01480.05720.0753-0.0234-0.0187-0.1940.0520.0679-0.1036-0.01790.0018-0.1427-0.0057-0.22-19.5775-10.21348.3176
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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