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- PDB-4k95: Crystal Structure of Parkin -

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Basic information

Entry
Database: PDB / ID: 4k95
TitleCrystal Structure of Parkin
ComponentsE3 ubiquitin-protein ligase parkin
KeywordsLIGASE / Ubiquitin-like domain / RING domains / zinc fingers / RBR ubiquitin ligase / zinc finger / UbcH7 / ubiquitin / mitochondria
Function / homology
Function and homology information


Josephin domain DUBs / Regulation of necroptotic cell death / Aggrephagy / PINK1-PRKN Mediated Mitophagy / 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 ...Josephin domain DUBs / Regulation of necroptotic cell death / Aggrephagy / PINK1-PRKN Mediated Mitophagy / 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 / cellular response to L-glutamine / negative regulation of exosomal secretion / negative regulation of glucokinase activity / mitochondrion to lysosome vesicle-mediated transport / type 2 mitophagy / response to curcumin / negative regulation of mitochondrial fusion / cellular response to hydrogen sulfide / Parkin-FBXW7-Cul1 ubiquitin ligase complex / free ubiquitin chain polymerization / positive regulation of protein linear polyubiquitination / host-mediated suppression of viral genome replication / RBR-type E3 ubiquitin transferase / positive regulation of mitophagy / F-box domain binding / positive regulation of mitochondrial fusion / negative regulation of actin filament bundle assembly / mitochondrial fragmentation involved in apoptotic process / regulation of cellular response to oxidative stress / mitochondrion localization / positive regulation of dendrite extension / regulation of dopamine metabolic process / negative regulation of excitatory postsynaptic potential / regulation of neurotransmitter secretion / protein K6-linked ubiquitination / norepinephrine metabolic process / dopaminergic synapse / autophagy of mitochondrion / positive regulation of type 2 mitophagy / protein localization to mitochondrion / synaptic transmission, dopaminergic / positive regulation of proteasomal protein catabolic process / positive regulation of protein localization to membrane / cellular response to toxic substance / mitochondrial fission / positive regulation of tumor necrosis factor-mediated signaling pathway / protein K11-linked ubiquitination / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / aggresome assembly / cellular response to L-glutamate / regulation of mitochondrion organization / negative regulation of synaptic transmission, glutamatergic / ubiquitin conjugating enzyme binding / negative regulation of JNK cascade / positive regulation of mitochondrial membrane potential / aggresome / regulation of reactive oxygen species metabolic process / response to corticosterone / positive regulation of mitochondrial fission / response to muscle activity / negative regulation of release of cytochrome c from mitochondria / ubiquitin-specific protease binding / dopamine uptake involved in synaptic transmission / intracellular vesicle / startle response / dopamine metabolic process / positive regulation of ATP biosynthetic process / cullin family protein binding / negative regulation of reactive oxygen species metabolic process / protein K63-linked ubiquitination / regulation of protein ubiquitination / protein monoubiquitination / regulation of synaptic vesicle endocytosis / response to unfolded protein / ubiquitin ligase complex / negative regulation of mitochondrial fission / positive regulation of insulin secretion involved in cellular response to glucose stimulus / regulation of postsynaptic membrane neurotransmitter receptor levels / protein K48-linked ubiquitination / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / proteasomal protein catabolic process / phospholipase binding / protein autoubiquitination / mitophagy / negative regulation of reactive oxygen species biosynthetic process / cellular response to manganese ion / heat shock protein binding / Hsp70 protein binding / tubulin binding / response to endoplasmic reticulum stress / ubiquitin binding / adult locomotory behavior / regulation of mitochondrial membrane potential / learning / mitochondrion organization / synaptic transmission, glutamatergic / PDZ domain binding / locomotory behavior
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. / 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 speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6.499 Å
AuthorsSeirafi, M. / Menade, M. / Sauve, V. / Kozlov, G. / Trempe, J.-F. / Nagar, B. / Gehring, K.
CitationJournal: Science / Year: 2013
Title: Structure of parkin reveals mechanisms for ubiquitin ligase activation.
Authors: Trempe, J.F. / Sauve, V. / Grenier, K. / Seirafi, M. / Tang, M.Y. / Menade, M. / Al-Abdul-Wahid, S. / Krett, J. / Wong, K. / Kozlov, G. / Nagar, B. / Fon, E.A. / Gehring, K.
History
DepositionApr 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Jul 10, 2013Group: Database references
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_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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase parkin
B: E3 ubiquitin-protein ligase parkin
C: E3 ubiquitin-protein ligase parkin
D: E3 ubiquitin-protein ligase parkin
E: E3 ubiquitin-protein ligase parkin
F: E3 ubiquitin-protein ligase parkin
G: E3 ubiquitin-protein ligase parkin
H: E3 ubiquitin-protein ligase parkin
I: E3 ubiquitin-protein ligase parkin
J: E3 ubiquitin-protein ligase parkin
K: E3 ubiquitin-protein ligase parkin
L: E3 ubiquitin-protein ligase parkin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)632,141108
Polymers625,86112
Non-polymers6,27996
Water00
1
A: E3 ubiquitin-protein ligase parkin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6789
Polymers52,1551
Non-polymers5238
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: E3 ubiquitin-protein ligase parkin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6789
Polymers52,1551
Non-polymers5238
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: E3 ubiquitin-protein ligase parkin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6789
Polymers52,1551
Non-polymers5238
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: E3 ubiquitin-protein ligase parkin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6789
Polymers52,1551
Non-polymers5238
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: E3 ubiquitin-protein ligase parkin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6789
Polymers52,1551
Non-polymers5238
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: E3 ubiquitin-protein ligase parkin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6789
Polymers52,1551
Non-polymers5238
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: E3 ubiquitin-protein ligase parkin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6789
Polymers52,1551
Non-polymers5238
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: E3 ubiquitin-protein ligase parkin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6789
Polymers52,1551
Non-polymers5238
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: E3 ubiquitin-protein ligase parkin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6789
Polymers52,1551
Non-polymers5238
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: E3 ubiquitin-protein ligase parkin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6789
Polymers52,1551
Non-polymers5238
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: E3 ubiquitin-protein ligase parkin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6789
Polymers52,1551
Non-polymers5238
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: E3 ubiquitin-protein ligase parkin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6789
Polymers52,1551
Non-polymers5238
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)208.598, 277.439, 125.891
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
E3 ubiquitin-protein ligase parkin


Mass: 52155.113 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Details: Codon-optimized for E.coli expression / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Park2, Prkn / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
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.: 96 / Source method: obtained synthetically / Formula: Zn

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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: 2.91 Å3/Da / Density % sol: 57.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 22.5% PEG3350, 0.2 M (NH4)2SO4, 0.1 M HEPES pH 7.0, 10% (v/v) glycerol, 3% sorbitol and 25 mM 2-mercaptoethanol, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9183 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 11, 2012 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9183 Å / Relative weight: 1
ReflectionResolution: 6.5→50 Å / Num. all: 14952 / Num. obs: 14922 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.2 % / Biso Wilson estimate: 227 Å2 / Rmerge(I) obs: 0.172 / Χ2: 1.574 / Net I/σ(I): 15.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
6.5-6.737.30.8052.514631.081100
6.73-77.40.683.214751.154100
7-7.327.50.5523.914541.159100
7.32-7.77.40.435.314741.194100
7.7-8.187.40.3416.714771.22100
8.18-8.817.40.20711.514751.378100
8.81-9.697.30.15417.115121.636100
9.69-11.087.20.11624.914901.965100
11.08-13.9170.09432.615452.131100
13.91-506.10.0840.115873.04198.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries: 4K7D (rat parkin 141-465) and 2ZEQ (mouse parkin 1-72)

4k7d

2zeq


Resolution: 6.499→49.334 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7121 / SU ML: 1.11 / σ(F): 1.34 / Phase error: 34.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3266 749 5.04 %random
Rwork0.3068 ---
obs0.3078 14865 99.4 %-
all-14952 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 213.59 Å2 / Biso mean: 88.6785 Å2 / Biso min: 28.1 Å2
Refinement stepCycle: LAST / Resolution: 6.499→49.334 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms35328 0 96 0 35424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01136972
X-RAY DIFFRACTIONf_angle_d1.17450148
X-RAY DIFFRACTIONf_chiral_restr0.0795196
X-RAY DIFFRACTIONf_plane_restr0.0056648
X-RAY DIFFRACTIONf_dihedral_angle_d14.79513632
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
6.4986-6.99910.37991590.369427672926292699
6.9991-7.70110.37321600.3526276429242924100
7.7011-8.80990.34711440.3332280729512951100
8.8099-11.07880.32981430.2914285129942994100
11.0788-49.33550.28171430.272529273070307098

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