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- PDB-3b1l: Crystal Structure of parkin ubiquitin-like domain R33Q mutant -

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Basic information

Entry
Database: PDB / ID: 3b1l
TitleCrystal Structure of parkin ubiquitin-like domain R33Q mutant
ComponentsE3 ubiquitin-protein ligase parkin
KeywordsLIGASE / Parkin / Ubiquitin / proteasome / Alfa-Beta-protein
Function / homology
Function and homology information


positive regulation of neurotransmitter uptake / regulation protein catabolic process at presynapse / negative regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway / mitochondrion-derived vesicle / negative regulation of spontaneous neurotransmitter secretion / negative regulation of intralumenal vesicle formation / PINK1-PRKN Mediated Mitophagy / negative regulation of exosomal secretion / Josephin domain DUBs / mitochondrion to lysosome vesicle-mediated transport ...positive regulation of neurotransmitter uptake / regulation protein catabolic process at presynapse / negative regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway / mitochondrion-derived vesicle / negative regulation of spontaneous neurotransmitter secretion / negative regulation of intralumenal vesicle formation / PINK1-PRKN Mediated Mitophagy / negative regulation of exosomal secretion / Josephin domain DUBs / mitochondrion to lysosome vesicle-mediated transport / positive regulation of mitochondrial fusion / Regulation of necroptotic cell death / parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization / cellular response to hydrogen sulfide / Aggrephagy / Parkin-FBXW7-Cul1 ubiquitin ligase complex / negative regulation of mitochondrial fusion / free ubiquitin chain polymerization / negative regulation of actin filament bundle assembly / RBR-type E3 ubiquitin transferase / positive regulation of protein linear polyubiquitination / F-box domain binding / negative regulation by host of viral genome replication / mitochondrion localization / positive regulation of mitophagy / mitochondrial fragmentation involved in apoptotic process / cellular response to toxic substance / regulation of dopamine metabolic process / dopaminergic synapse / regulation of cellular response to oxidative stress / negative regulation of excitatory postsynaptic potential / regulation of neurotransmitter secretion / cellular response to L-glutamate / autophagy of mitochondrion / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Antigen processing: Ubiquitination & Proteasome degradation / protein K6-linked ubiquitination / positive regulation of dendrite extension / norepinephrine metabolic process / protein localization to mitochondrion / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / negative regulation of JNK cascade / positive regulation of protein localization to membrane / negative regulation of synaptic transmission, glutamatergic / protein K11-linked ubiquitination / protein metabolic process / synaptic transmission, dopaminergic / positive regulation of tumor necrosis factor-mediated signaling pathway / mitochondrial fission / aggresome assembly / ubiquitin conjugating enzyme binding / regulation of mitochondrion organization / aggresome / positive regulation of mitochondrial membrane potential / regulation of synaptic vesicle endocytosis / dopamine uptake involved in synaptic transmission / positive regulation of mitochondrial fission / dopamine metabolic process / intracellular vesicle / ubiquitin-specific protease binding / positive regulation of ATP biosynthetic process / startle response / negative regulation of release of cytochrome c from mitochondria / regulation of postsynaptic membrane neurotransmitter receptor levels / protein monoubiquitination / protein K63-linked ubiquitination / positive regulation of insulin secretion involved in cellular response to glucose stimulus / phospholipase binding / cullin family protein binding / mitophagy / negative regulation of mitochondrial fission / negative regulation of insulin secretion / protein autoubiquitination / protein K48-linked ubiquitination / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of reactive oxygen species biosynthetic process / ubiquitin ligase complex / Hsp70 protein binding / response to endoplasmic reticulum stress / mitochondrion organization / tubulin binding / adult locomotory behavior / negative regulation of protein phosphorylation / locomotory behavior / regulation of mitochondrial membrane potential / ubiquitin binding / learning / synaptic transmission, glutamatergic / regulation of autophagy / G protein-coupled receptor binding / PDZ domain binding / protein destabilization / protein catabolic process / modulation of chemical synaptic transmission / negative regulation of canonical Wnt signaling pathway / terminal bouton / synaptic vesicle membrane / beta-catenin binding / kinase binding / histone deacetylase 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 / 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. / 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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsTomoo, K. / Ikemiya, A. / Amami, Y. / In, Y. / Ishida, T.
CitationJournal: to be published
Title: Crystal Structure of parkin ubiquitin-like domain R33Q mutant
Authors: Tomoo, K. / Ikemiya, A. / Amami, Y. / In, Y. / Ishida, T.
History
DepositionJul 4, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2018Group: Data collection / Source and taxonomy / Structure summary
Category: entity / entity_src_gen / entity_src_nat / Item: _entity.src_method
Revision 1.2Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: E3 ubiquitin-protein ligase parkin


Theoretical massNumber of molelcules
Total (without water)8,7011
Polymers8,7011
Non-polymers00
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.790, 45.790, 65.980
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein E3 ubiquitin-protein ligase parkin


Mass: 8700.982 Da / Num. of mol.: 1 / Fragment: Ubiquitin-like domain / Mutation: R33Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
References: UniProt: Q9WVS6, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.29 Å3/Da / Density % sol: 46.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 3M NaCl, 100mM acetate buffer, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→33.99 Å / Num. all: 6738 / Num. obs: 6718 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 5.42 % / Rmerge(I) obs: 0.079

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→25.36 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.913 / Occupancy max: 1 / Occupancy min: 1 / SU B: 2.979 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2429 320 4.8 %RANDOM
Rwork0.1885 ---
obs0.1908 6708 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 57.43 Å2 / Biso mean: 17.9307 Å2 / Biso min: 7.71 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2---0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.85→25.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms612 0 0 33 645
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.022622
X-RAY DIFFRACTIONr_angle_refined_deg2.0591.957842
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.559575
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.23624.06332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.97415112
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.413156
X-RAY DIFFRACTIONr_chiral_restr0.1480.297
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021474
X-RAY DIFFRACTIONr_mcbond_it1.2041.5381
X-RAY DIFFRACTIONr_mcangle_it2.1762625
X-RAY DIFFRACTIONr_scbond_it4.0343241
X-RAY DIFFRACTIONr_scangle_it6.8964.5217
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 27 -
Rwork0.25 464 -
all-491 -
obs--99.8 %

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