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- PDB-5c1z: Parkin (UblR0RBR) -

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Basic information

Entry
Database: PDB / ID: 5c1z
TitleParkin (UblR0RBR)
ComponentsE3 ubiquitin-protein ligase parkin
KeywordsLIGASE
Function / homology
Function and homology information


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 primary amine oxidase activity / negative regulation of spontaneous neurotransmitter secretion / negative regulation of intralumenal vesicle formation / regulation of protein targeting to mitochondrion / negative regulation of glucokinase 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 primary amine oxidase activity / negative regulation of spontaneous neurotransmitter secretion / negative regulation of intralumenal vesicle formation / regulation of protein targeting to mitochondrion / negative regulation of glucokinase activity / mitochondrion to lysosome vesicle-mediated transport / negative regulation of exosomal secretion / positive regulation of mitochondrial fusion / parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization / protein K29-linked ubiquitination / Lewy body / protein K27-linked ubiquitination / Parkin-FBXW7-Cul1 ubiquitin ligase complex / free ubiquitin chain polymerization / negative regulation of actin filament bundle assembly / regulation of synaptic vesicle transport / negative regulation of mitochondrial fusion / RBR-type E3 ubiquitin transferase / positive regulation of mitophagy in response to mitochondrial depolarization / positive regulation of protein linear polyubiquitination / F-box domain binding / negative regulation by host of viral genome replication / norepinephrine metabolic process / cellular response to toxic substance / dopaminergic synapse / regulation of dopamine metabolic process / regulation of necroptotic process / regulation of cellular response to oxidative stress / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / protein K6-linked ubiquitination / positive regulation of autophagy of mitochondrion / positive regulation of dendrite extension / positive regulation of proteasomal protein catabolic process / protein localization to mitochondrion / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / positive regulation of protein localization to membrane / negative regulation of JNK cascade / protein K11-linked ubiquitination / cellular response to dopamine / positive regulation of tumor necrosis factor-mediated signaling pathway / ERAD pathway / mitochondrial fission / aggresome assembly / ubiquitin conjugating enzyme binding / regulation of canonical Wnt signaling pathway / aggresome / regulation of mitochondrion organization / dopamine uptake involved in synaptic transmission / regulation of reactive oxygen species metabolic process / regulation of synaptic vesicle endocytosis / startle response / positive regulation of mitochondrial fission / autophagy of mitochondrion / dopamine metabolic process / regulation of dopamine secretion / protein monoubiquitination / ubiquitin-specific protease binding / mitophagy / negative regulation of release of cytochrome c from mitochondria / cullin family protein binding / protein K63-linked ubiquitination / phospholipase binding / regulation of protein ubiquitination / regulation of glucose metabolic process / protein K48-linked ubiquitination / negative regulation of insulin secretion / negative regulation of reactive oxygen species metabolic process / positive regulation of DNA binding / cellular response to unfolded protein / cellular response to manganese ion / protein autoubiquitination / ubiquitin ligase complex / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / mitochondrion organization / heat shock protein binding / response to endoplasmic reticulum stress / PINK1-PRKN Mediated Mitophagy / adult locomotory behavior / tubulin binding / Josephin domain DUBs / Hsp70 protein binding / regulation of mitochondrial membrane potential / negative regulation of protein phosphorylation / learning / ubiquitin binding / central nervous system development / synaptic transmission, glutamatergic / regulation of autophagy / G protein-coupled receptor binding / PDZ domain binding / proteasomal protein catabolic process / macroautophagy / negative regulation of canonical Wnt signaling pathway / protein destabilization / regulation of protein stability
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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 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)92,92826
Polymers91,2502
Non-polymers1,67824
Water12,809711
1
A: E3 ubiquitin-protein ligase parkin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,46413
Polymers45,6251
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)46,46413
Polymers45,6251
Non-polymers83912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.310, 67.320, 206.230
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: 45625.012 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, 735 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 / Sulfate


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 / Glycerol


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


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


Mass: 18.015 Da / Num. of mol.: 711 / 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: 2.56 Å3/Da / Density % sol: 51.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 5.5 / Details: LiSO4, PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9174 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9174 Å / Relative weight: 1
ReflectionResolution: 1.79→56.36 Å / Num. all: 87826 / Num. obs: 87891 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 32.3 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 11.2
Reflection shellResolution: 1.79→1.85 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 1.8 / % possible all: 97.6

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
iMOSFLMdata reduction
SCALAdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K95
Resolution: 1.79→56.36 Å / Cor.coef. Fo:Fc: 0.9505 / Cor.coef. Fo:Fc free: 0.9461 / SU R Cruickshank DPI: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.124 / SU Rfree Blow DPI: 0.111 / SU Rfree Cruickshank DPI: 0.107
RfactorNum. reflection% reflectionSelection details
Rfree0.2123 4270 4.86 %RANDOM
Rwork0.1915 ---
obs0.1925 87826 98.42 %-
Displacement parametersBiso mean: 49.13 Å2
Baniso -1Baniso -2Baniso -3
1--4.8921 Å20 Å20 Å2
2---3.9323 Å20 Å2
3---8.8245 Å2
Refine analyzeLuzzati coordinate error obs: 0.255 Å
Refinement stepCycle: 1 / Resolution: 1.79→56.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6180 0 52 711 6943
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0086381HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.948677HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2239SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes170HARMONIC2
X-RAY DIFFRACTIONt_gen_planes958HARMONIC5
X-RAY DIFFRACTIONt_it6381HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.78
X-RAY DIFFRACTIONt_other_torsion17.86
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion805SEMIHARMONIC5
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_contact7754SEMIHARMONIC4
LS refinement shellResolution: 1.79→1.84 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 292 4.59 %
Rwork0.2243 6072 -
all0.2245 6364 -
obs--98.42 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.9566-0.4301-1.28370.60940.58671.9418-0.1624-0.0006-0.0999-0.0386-0.00620.05280.2089-0.04540.16860.0044-0.0067-0.0038-0.0353-0.0096-0.064-13.210510.38428.1537
20.5887-0.42570.57710.9742-1.28221.8729-0.0094-0.04160.0489-0.0016-0.1606-0.0994-0.05170.20690.17-0.0317-0.0069-0.00960.015-0.0022-0.063-27.2312-3.622543.3544
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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