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- PDB-4i1f: Structure of Parkin-S223P E3 ligase -

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Basic information

Entry
Database: PDB / ID: 4i1f
TitleStructure of Parkin-S223P E3 ligase
ComponentsE3 ubiquitin-protein ligase parkin
KeywordsLIGASE / RBR E3 ubiquitin ligase
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 / regulation protein catabolic process at presynapse / negative regulation of spontaneous neurotransmitter secretion / negative regulation of intralumenal vesicle formation / cellular response to L-glutamine / regulation of protein localization to mitochondrion / 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 / regulation protein catabolic process at presynapse / negative regulation of spontaneous neurotransmitter secretion / negative regulation of intralumenal vesicle formation / cellular response to L-glutamine / regulation of protein localization to mitochondrion / negative regulation of exosomal secretion / mitochondrion to lysosome vesicle-mediated transport / type 2 mitophagy / aggresome assembly / negative regulation of glucokinase activity / response to curcumin / protein K29-linked ubiquitination / free ubiquitin chain polymerization / cellular response to hydrogen sulfide / negative regulation of mitochondrial fusion / positive regulation of protein linear polyubiquitination / RBR-type E3 ubiquitin transferase / regulation of dopamine metabolic process / Parkin-FBXW7-Cul1 ubiquitin ligase complex / positive regulation of mitochondrial fusion / negative regulation of actin filament bundle assembly / regulation of synaptic vesicle transport / mitochondrial fragmentation involved in apoptotic process / host-mediated suppression of viral genome replication / positive regulation of mitophagy / F-box domain binding / regulation of necroptotic process / regulation of cellular response to oxidative stress / positive regulation of dendrite extension / positive regulation of type 2 mitophagy / cellular response to L-glutamate / autophagy of mitochondrion / negative regulation of excitatory postsynaptic potential / dopaminergic synapse / mitochondrial fission / aggresome / mitochondrion localization / cellular response to dopamine / cellular response to toxic substance / positive regulation of tumor necrosis factor-mediated signaling pathway / regulation of mitochondrion organization / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / positive regulation of protein localization to membrane / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / protein K11-linked ubiquitination / protein K6-linked ubiquitination / positive regulation of proteasomal protein catabolic process / neuron cellular homeostasis / negative regulation of JNK cascade / negative regulation of reactive oxygen species metabolic process / ubiquitin conjugating enzyme binding / negative regulation of synaptic transmission, glutamatergic / regulation of reactive oxygen species metabolic process / positive regulation of mitochondrial membrane potential / regulation of canonical Wnt signaling pathway / protein K27-linked ubiquitination / response to muscle activity / positive regulation of mitochondrial fission / negative regulation of release of cytochrome c from mitochondria / response to corticosterone / protein localization to mitochondrion / dopamine metabolic process / ubiquitin-specific protease binding / Lewy body / regulation of glucose metabolic process / positive regulation of ATP biosynthetic process / cellular response to unfolded protein / regulation of protein ubiquitination / regulation of dopamine secretion / negative regulation of insulin secretion / protein monoubiquitination / cullin family protein binding / regulation of synaptic vesicle endocytosis / protein deubiquitination / mitophagy / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / regulation of postsynaptic membrane neurotransmitter receptor levels / negative regulation of mitochondrial fission / adult locomotory behavior / protein K63-linked ubiquitination / protein autoubiquitination / negative regulation of reactive oxygen species biosynthetic process / phospholipase binding / ubiquitin ligase complex / cellular response to manganese ion / ERAD pathway / heat shock protein binding / protein K48-linked ubiquitination / response to endoplasmic reticulum stress / Hsp70 protein binding / macroautophagy / central nervous system development / positive regulation of insulin secretion involved in cellular response to glucose stimulus / mitochondrion organization / 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. / 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 / SYNCHROTRON / MAD / Resolution: 1.58 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 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _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)37,10910
Polymers36,4491
Non-polymers6619
Water4,810267
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.955, 133.155, 65.385
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 36448.648 Da / Num. of mol.: 1 / Fragment: R0RBR (UNP residues 141-465) / Mutation: S223P
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: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ba
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.6 Å3/Da / Density % sol: 52.63 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, pH 7.5, 20% PEG4000, 10% isopropanol, 10 mM barium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.2831, 1.2699
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 6, 2012
RadiationMonochromator: Khozu double flat crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.28311
21.26991
ReflectionResolution: 1.58→73 Å / Num. all: 52798 / Num. obs: 52033 / % possible obs: 98.55 % / Redundancy: 6.9 % / Rsym value: 0.078 / Net I/σ(I): 11
Reflection shellResolution: 1.58→1.67 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.99 / Mean I/σ(I) obs: 1.6 / Rsym value: 0.99 / % possible all: 99.8

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Processing

Software
NameVersionClassification
SHELXmodel building
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.58→72.81 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.937 / SU B: 1.607 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24528 2650 5.1 %RANDOM
Rwork0.20508 ---
obs0.20706 52033 99.46 %-
all-52033 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.743 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å20 Å20 Å2
2--0.12 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.58→72.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2400 0 9 267 2676
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0192466
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.261.9423342
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.555304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.09523.248117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.40415399
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.551520
X-RAY DIFFRACTIONr_chiral_restr0.1620.2349
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0211921
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: 1.58→1.621 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.478 194 -
Rwork0.429 3351 -
obs--98.31 %

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