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- PDB-4i1h: Structure of Parkin E3 ligase -

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Basic information

Entry
Database: PDB / ID: 4i1h
TitleStructure of Parkin E3 ligase
ComponentsE3 ubiquitin-protein ligase parkin
KeywordsLIGASE / RBR E3 ubiquitin ligase
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 / 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 / regulation of synaptic vesicle transport / negative regulation of mitochondrial fusion / free ubiquitin chain polymerization / negative regulation of actin filament bundle assembly / positive regulation of mitophagy in response to mitochondrial depolarization / RBR-type E3 ubiquitin transferase / positive regulation of protein linear polyubiquitination / F-box domain binding / negative regulation by host of viral genome replication / positive regulation of mitophagy / cellular response to toxic substance / regulation of dopamine metabolic process / regulation of necroptotic process / dopaminergic synapse / regulation of cellular response to oxidative stress / autophagy of mitochondrion / 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 / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / negative regulation of JNK cascade / positive regulation of protein localization to membrane / protein K11-linked ubiquitination / cellular response to dopamine / positive regulation of tumor necrosis factor-mediated signaling pathway / mitochondrial fission / aggresome assembly / ubiquitin conjugating enzyme binding / regulation of canonical Wnt signaling pathway / regulation of mitochondrion organization / aggresome / regulation of reactive oxygen species metabolic process / regulation of synaptic vesicle endocytosis / dopamine uptake involved in synaptic transmission / positive regulation of mitochondrial fission / dopamine metabolic process / regulation of dopamine secretion / ubiquitin-specific protease binding / startle response / negative regulation of release of cytochrome c from mitochondria / protein monoubiquitination / cullin family protein binding / phospholipase binding / protein K63-linked ubiquitination / mitophagy / regulation of protein ubiquitination / regulation of glucose metabolic process / negative regulation of reactive oxygen species metabolic process / cellular response to unfolded protein / proteasomal protein catabolic process / positive regulation of DNA binding / cellular response to manganese ion / negative regulation of insulin secretion / protein autoubiquitination / protein K48-linked ubiquitination / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / ERAD pathway / ubiquitin ligase complex / Hsp70 protein binding / heat shock protein binding / PINK1-PRKN Mediated Mitophagy / tubulin binding / response to endoplasmic reticulum stress / mitochondrion organization / adult locomotory behavior / Josephin domain DUBs / regulation of mitochondrial membrane potential / negative regulation of protein phosphorylation / learning / regulation of autophagy / ubiquitin binding / 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 / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLougheed, J.C. / Brecht, E. / Yao, N.H.
CitationJournal: Nat Commun / Year: 2013
Title: Structure and function of Parkin E3 ubiquitin ligase reveals aspects of RING and HECT ligases.
Authors: Riley, B.E. / Lougheed, J.C. / Callaway, K. / Velasquez, M. / Brecht, E. / Nguyen, L. / Shaler, T. / Walker, D. / Yang, Y. / Regnstrom, K. / Diep, L. / Zhang, Z. / Chiou, S. / Bova, M. / ...Authors: Riley, B.E. / Lougheed, J.C. / Callaway, K. / Velasquez, M. / Brecht, E. / Nguyen, L. / Shaler, T. / Walker, D. / Yang, Y. / Regnstrom, K. / Diep, L. / Zhang, Z. / Chiou, S. / Bova, M. / Artis, D.R. / Yao, N. / Baker, J. / Yednock, T. / Johnston, J.A.
History
DepositionNov 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)36,9629
Polymers36,4391
Non-polymers5238
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.110, 133.930, 66.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-710-

HOH

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Components

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


Mass: 36438.613 Da / Num. of mol.: 1 / Fragment: R0RBR (UNP residues 141-465)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARK2, PRKN / Production host: Escherichia coli (E. coli)
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.65 Å3/Da / Density % sol: 53.58 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Tris, pH 6.5, 0.2 M sodium chloride, 25% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 383K

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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 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→16.971 Å / Num. all: 26566 / Num. obs: 21783 / % possible obs: 82 % / Redundancy: 6.1 % / Rsym value: 0.111 / Net I/σ(I): 12.1
Reflection shellResolution: 2→2.11 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 3.6 / % possible all: 36.3

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Processing

Software
NameClassification
StructureStudiodata collection
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4I1F

4i1f


Resolution: 2→16.971 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.398 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.203 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21537 1089 5 %RANDOM
Rwork0.18068 ---
obs0.18239 21783 81.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.871 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å20 Å20 Å2
2--0.24 Å20 Å2
3---0.44 Å2
Refinement stepCycle: LAST / Resolution: 2→16.971 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2399 0 8 263 2670
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192467
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8421.9423343
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.755305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.5723.559118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.07115405
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9631519
X-RAY DIFFRACTIONr_chiral_restr0.1180.2350
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211920
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 30 -
Rwork0.216 523 -
obs-553 29.14 %

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