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- PDB-4zyn: Crystal Structure of Parkin E3 ubiquitin ligase (linker deletion;... -

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Basic information

Entry
Database: PDB / ID: 4zyn
TitleCrystal Structure of Parkin E3 ubiquitin ligase (linker deletion; delta 86-130)
ComponentsE3 ubiquitin-protein ligase parkin
KeywordsLIGASE / RING domains / Ubiquitin-like domain / RBR
Function / homology
Function and homology information


Josephin domain DUBs / Regulation of necroptotic cell death / Aggrephagy / PINK1-PRKN Mediated Mitophagy / cellular response to L-glutamine / positive regulation of neurotransmitter uptake / negative regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway / Antigen processing: Ubiquitination & Proteasome degradation / mitochondrion-derived vesicle / negative regulation of spontaneous neurotransmitter secretion ...Josephin domain DUBs / Regulation of necroptotic cell death / Aggrephagy / PINK1-PRKN Mediated Mitophagy / cellular response to L-glutamine / positive regulation of neurotransmitter uptake / negative regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway / Antigen processing: Ubiquitination & Proteasome degradation / mitochondrion-derived vesicle / negative regulation of spontaneous neurotransmitter secretion / negative regulation of intralumenal vesicle formation / regulation protein catabolic process at presynapse / response to curcumin / negative regulation of exosomal secretion / negative regulation of glucokinase activity / mitochondrion to lysosome vesicle-mediated transport / cellular response to hydrogen sulfide / type 2 mitophagy / negative regulation of actin filament bundle assembly / negative regulation of mitochondrial fusion / Parkin-FBXW7-Cul1 ubiquitin ligase complex / free ubiquitin chain polymerization / positive regulation of protein linear polyubiquitination / negative regulation by host of viral genome replication / positive regulation of mitophagy / RBR-type E3 ubiquitin transferase / mitochondrial fragmentation involved in apoptotic process / F-box domain binding / positive regulation of mitochondrial fusion / mitochondrion localization / regulation of cellular response to oxidative stress / negative regulation of excitatory postsynaptic potential / regulation of dopamine metabolic process / regulation of neurotransmitter secretion / 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 / cellular response to L-glutamate / 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 / synaptic transmission, dopaminergic / negative regulation of JNK cascade / mitochondrial fission / positive regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of synaptic transmission, glutamatergic / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / aggresome assembly / protein K11-linked ubiquitination / ubiquitin conjugating enzyme binding / regulation of mitochondrion organization / positive regulation of mitochondrial membrane potential / aggresome / regulation of reactive oxygen species metabolic process / response to corticosterone / positive regulation of mitochondrial fission / positive regulation of ATP biosynthetic process / response to muscle activity / dopamine uptake involved in synaptic transmission / intracellular vesicle / ubiquitin-specific protease binding / negative regulation of release of cytochrome c from mitochondria / startle response / dopamine metabolic process / phospholipase binding / regulation of synaptic vesicle endocytosis / cullin family protein binding / negative regulation of reactive oxygen species metabolic process / positive regulation of insulin secretion involved in cellular response to glucose stimulus / protein K63-linked ubiquitination / negative regulation of mitochondrial fission / protein monoubiquitination / regulation of protein ubiquitination / cellular response to manganese ion / ubiquitin ligase complex / response to unfolded protein / regulation of postsynaptic membrane neurotransmitter receptor levels / negative regulation of insulin secretion / proteasomal protein catabolic process / protein K48-linked ubiquitination / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / protein autoubiquitination / mitophagy / negative regulation of reactive oxygen species biosynthetic process / heat shock protein binding / Hsp70 protein binding / tubulin binding / response to endoplasmic reticulum stress / regulation of mitochondrial membrane potential / adult locomotory behavior / ubiquitin binding / learning / synaptic transmission, glutamatergic / PDZ domain binding / mitochondrion organization
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, a half RING-finger 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 speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsLilov, A. / Sauve, V. / Trempe, J.F. / Rodionov, D. / Wang, J. / Gehring, K.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-125924 Canada
CitationJournal: Embo J. / Year: 2015
Title: A Ubl/ubiquitin switch in the activation of Parkin.
Authors: Sauve, V. / Lilov, A. / Seirafi, M. / Vranas, M. / Rasool, S. / Kozlov, G. / Sprules, T. / Wang, J. / Trempe, J.F. / Gehring, K.
History
DepositionMay 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Data collection / Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: 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
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)96,29124
Polymers94,6682
Non-polymers1,62322
Water1,15364
1
A: E3 ubiquitin-protein ligase parkin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,24113
Polymers47,3341
Non-polymers90812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: E3 ubiquitin-protein ligase parkin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,04911
Polymers47,3341
Non-polymers71510
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.105, 114.105, 186.399
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein E3 ubiquitin-protein ligase parkin


Mass: 47333.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: deletion 86-130 / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Park2, Prkn / Plasmid: pGEX-6p1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q9JK66, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#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.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
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: 2.47 Å3/Da / Density % sol: 50.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.3M Ammonium Sulfate, 0.1M HEPES pH 7.5, 18% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Nov 28, 2012
RadiationMonochromator: Rigaku VariMax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.54→50 Å / Num. obs: 28338 / % possible obs: 95 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.047 / Rrim(I) all: 0.131 / Χ2: 1.108 / Net I/av σ(I): 12.158 / Net I/σ(I): 6.2 / Num. measured all: 230168
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allCC1/2Χ2% possible allRpim(I) allRmerge(I) obsRrim(I) all
2.54-2.582.710400.1230.82569
2.58-2.63311350.1290.87977.5
2.63-2.683.412360.1041.182.2
2.68-2.743.913150.2250.92987.40.915
2.74-2.84.613480.3270.87591.60.781
2.8-2.865.214250.3810.91994.70.578
2.86-2.93614790.5170.9598.10.4220.963
2.93-3.017.214580.6870.92799.90.3240.8150.879
3.01-3.19.314990.830.9251000.2320.6750.714
3.1-3.210.114770.8940.9841000.1540.4680.493
3.2-3.3110.115000.930.9491000.1150.3480.367
3.31-3.4510.214980.9651.0911000.0920.2790.294
3.45-3.610.214810.9681.0391000.080.2440.257
3.6-3.7910.215040.9861.1461000.0630.1920.202
3.79-4.0310.214930.9891.2121000.0460.140.148
4.03-4.3410.314680.9941.1471000.0350.1060.112
4.34-4.7810.315090.9961.1681000.0280.0870.091
4.78-5.4710.314940.9971.151000.0260.0810.085
5.47-6.8910.414890.9971.1431000.0230.0710.075
6.89-5010.314900.9991.80999.70.0150.0460.048

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
StructureStudiodata collection
PDB_EXTRACT3.15data extraction
XDSdata scaling
MOLREPphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K7D

4k7d


Resolution: 2.54→36.62 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.918 / WRfactor Rfree: 0.2326 / WRfactor Rwork: 0.1874 / FOM work R set: 0.9021 / SU B: 7.373 / SU ML: 0.095 / SU R Cruickshank DPI: 0.1172 / SU Rfree: 0.0589 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2353 1485 5 %RANDOM
Rwork0.1925 ---
obs0.1947 28036 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 235.59 Å2 / Biso mean: 66.684 Å2 / Biso min: 5.54 Å2
Baniso -1Baniso -2Baniso -3
1-1.9 Å20 Å20 Å2
2--1.9 Å20 Å2
3----3.79 Å2
Refinement stepCycle: final / Resolution: 2.54→36.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5673 0 46 64 5783
Biso mean--91.87 36.64 -
Num. residues----752
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0195879
X-RAY DIFFRACTIONr_bond_other_d0.0030.025214
X-RAY DIFFRACTIONr_angle_refined_deg1.3321.9367986
X-RAY DIFFRACTIONr_angle_other_deg0.968311969
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.775748
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.78123.829269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.47115873
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4161537
X-RAY DIFFRACTIONr_chiral_restr0.070.2861
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216815
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021422
X-RAY DIFFRACTIONr_mcbond_it1.965.6433010
X-RAY DIFFRACTIONr_mcbond_other1.965.6443009
X-RAY DIFFRACTIONr_mcangle_it3.3348.4363743
LS refinement shellResolution: 2.541→2.607 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 106 -
Rwork0.159 1900 -
all-2006 -
obs--90.28 %
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)
12.21480.75610.23281.7821.535.26260.0438-0.0976-0.0806-0.0609-0.2210.2631-0.0903-0.69150.17720.03620.0110.02170.1684-0.02690.140420.18715.748-30.777
20.7195-0.03550.67981.5366-0.99481.276-0.03910.00450.00080.1673-0.0378-0.1344-0.1241-0.01110.07690.0655-0.02840.03280.0583-0.00910.107750.9420.186-1.006
31.7555-1.20480.27562.19340.71640.765-0.0208-0.0475-0.12910.13570.0480.21230.0703-0.0687-0.02720.0716-0.03010.06870.06490.02640.129730.8112.11-11.651
49.02682.04199.89580.46412.245210.8724-0.29710.85490.1043-0.09160.16580.0271-0.40780.82690.13130.41750.32570.19030.84120.05550.63484.61927.115-15.263
57.8122-1.5721-2.36960.39620.17062.654-0.055-0.6925-1.2018-0.15760.30580.20840.8807-0.2346-0.25080.7653-0.1122-0.04780.5637-0.14641.037341.848-3.267-17.525
62.5146-0.2941-0.43170.75090.57185.3401-0.1026-0.0833-0.0053-0.0006-0.045-0.00130.038-0.25650.14760.0475-0.00090.00340.0298-0.01790.105624.51-11.73530.498
70.9788-0.2889-0.60050.7568-0.47321.0529-0.06110.0288-0.0489-0.0212-0.0837-0.0880.06020.02160.14480.0558-0.0068-0.01460.0388-0.0040.113853.14-19.3560.972
80.98350.3298-0.11591.29980.43130.2018-0.03260.08490.0424-0.0706-0.00450.1156-0.0139-0.0150.0370.03650.015-0.04310.0380.02190.131134.58-8.13911.646
95.16480.2855-5.01649.85010.1625.3945-0.104-0.6362-0.63770.5652-0.64890.95050.17030.17410.75290.2998-0.13190.13870.6301-0.33460.66546.141-19.86813.727
107.7598-3.4208-1.43423.84511.29461.97430.05850.25090.4655-0.22410.0411-0.6067-0.16710.523-0.09970.2825-0.0072-0.05930.2078-0.00510.313948.0944.46517.622
112.4315-0.41310.0242.3129-0.11510.4242-0.02850.05530.03770.09440.0105-0.10950.0852-0.10670.01810.0764-0.03490.00780.04040.01590.056965.1566.916-6.519
121.5349-0.074-0.34631.12990.29140.8356-0.14380.03170.07890.03470.12950.0285-0.0678-0.07490.01430.04880.0036-0.02510.04450.03560.110469.165-8.576.403
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 77
2X-RAY DIFFRACTION2A140 - 227
3X-RAY DIFFRACTION2A501 - 502
4X-RAY DIFFRACTION3A228 - 327
5X-RAY DIFFRACTION3A503 - 504
6X-RAY DIFFRACTION4A328 - 378
7X-RAY DIFFRACTION4A505 - 506
8X-RAY DIFFRACTION5A392 - 413
9X-RAY DIFFRACTION6B1 - 77
10X-RAY DIFFRACTION7B140 - 227
11X-RAY DIFFRACTION7B501 - 502
12X-RAY DIFFRACTION8B228 - 327
13X-RAY DIFFRACTION8B503 - 504
14X-RAY DIFFRACTION9B328 - 378
15X-RAY DIFFRACTION9B505 - 506
16X-RAY DIFFRACTION10B392 - 413
17X-RAY DIFFRACTION11A414 - 465
18X-RAY DIFFRACTION11A507 - 508
19X-RAY DIFFRACTION12B414 - 465
20X-RAY DIFFRACTION12B507 - 508

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