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- PDB-4k7d: Crystal Structure of Parkin C-terminal RING domains -

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Basic information

Entry
Database: PDB / ID: 4k7d
TitleCrystal Structure of Parkin C-terminal RING domains
ComponentsE3 ubiquitin-protein ligase parkin
KeywordsLIGASE / RING domains / zinc fingers / RBR ubiquitin ligase / E3 ubiquitin protein ligase / Ubiquitin / UbcH7
Function / homology
Function and homology information


Josephin domain DUBs / Regulation of necroptotic cell death / Aggrephagy / PINK1-PRKN Mediated Mitophagy / cellular response to L-glutamine / 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 ...Josephin domain DUBs / Regulation of necroptotic cell death / Aggrephagy / PINK1-PRKN Mediated Mitophagy / cellular response to L-glutamine / 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 / response to curcumin / negative regulation of exosomal secretion / negative regulation of glucokinase activity / mitochondrion to lysosome vesicle-mediated transport / cellular response to hydrogen sulfide / type 2 mitophagy / negative regulation of actin filament bundle assembly / negative regulation of mitochondrial fusion / Parkin-FBXW7-Cul1 ubiquitin ligase complex / free ubiquitin chain polymerization / positive regulation of protein linear polyubiquitination / negative regulation by host of viral genome replication / positive regulation of mitophagy / RBR-type E3 ubiquitin transferase / mitochondrial fragmentation involved in apoptotic process / F-box domain binding / positive regulation of mitochondrial fusion / mitochondrion localization / regulation of cellular response to oxidative stress / negative regulation of excitatory postsynaptic potential / regulation of dopamine metabolic process / regulation of neurotransmitter secretion / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / dopaminergic synapse / positive regulation of dendrite extension / protein K6-linked ubiquitination / positive regulation of protein localization to membrane / cellular response to L-glutamate / autophagy of mitochondrion / norepinephrine metabolic process / cellular response to toxic substance / positive regulation of type 2 mitophagy / protein localization to mitochondrion / positive regulation of proteasomal protein catabolic process / synaptic transmission, dopaminergic / negative regulation of JNK cascade / mitochondrial fission / positive regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of synaptic transmission, glutamatergic / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / aggresome assembly / protein K11-linked ubiquitination / ubiquitin conjugating enzyme binding / regulation of mitochondrion organization / positive regulation of mitochondrial membrane potential / aggresome / regulation of reactive oxygen species metabolic process / response to corticosterone / positive regulation of mitochondrial fission / positive regulation of ATP biosynthetic process / response to muscle activity / dopamine uptake involved in synaptic transmission / intracellular vesicle / ubiquitin-specific protease binding / negative regulation of release of cytochrome c from mitochondria / startle response / dopamine metabolic process / phospholipase binding / regulation of synaptic vesicle endocytosis / cullin family protein binding / negative regulation of reactive oxygen species metabolic process / positive regulation of insulin secretion involved in cellular response to glucose stimulus / protein K63-linked ubiquitination / negative regulation of mitochondrial fission / protein monoubiquitination / regulation of protein ubiquitination / cellular response to manganese ion / ubiquitin ligase complex / response to unfolded protein / regulation of postsynaptic membrane neurotransmitter receptor levels / negative regulation of insulin secretion / proteasomal protein catabolic process / protein K48-linked ubiquitination / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / protein autoubiquitination / mitophagy / negative regulation of reactive oxygen species biosynthetic process / heat shock protein binding / Hsp70 protein binding / tubulin binding / response to endoplasmic reticulum stress / regulation of mitochondrial membrane potential / adult locomotory behavior / ubiquitin binding / learning / synaptic transmission, glutamatergic / PDZ domain binding / mitochondrion organization
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
MALONATE ION / E3 ubiquitin-protein ligase parkin
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsSauve, V. / Trempe, J.-F. / Menade, M. / 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 17, 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 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,40531
Polymers110,4933
Non-polymers1,91128
Water81145
1
A: E3 ubiquitin-protein ligase parkin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,45610
Polymers36,8311
Non-polymers6259
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: E3 ubiquitin-protein ligase parkin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,45610
Polymers36,8311
Non-polymers6259
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: E3 ubiquitin-protein ligase parkin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,49211
Polymers36,8311
Non-polymers66110
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.700, 106.625, 154.216
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein E3 ubiquitin-protein ligase parkin


Mass: 36831.070 Da / Num. of mol.: 3 / Fragment: C-terminal RING domains (141-465)
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.: 24 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H2O4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 3.15 Å3/Da / Density % sol: 60.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.9 M sodium malonate pH 7.0, 0.1 M HEPES pH 7.0, 5% (v/v) glycerol, 56 mM 2-mercaptoethanol, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.2824 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 16, 2012 / Details: Vertical focusing mirrors
RadiationMonochromator: ACCEL/BRUKER DCM, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2824 Å / Relative weight: 1
ReflectionResolution: 2.8→53.33 Å / Num. all: 35155 / Num. obs: 35121 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 9.7 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 19.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.8-2.959.70.4641.64874850440.464100
2.95-3.139.70.2792.64685248060.279100
3.13-3.359.80.154.94379644880.15100
3.35-3.619.80.0947.44111642160.094100
3.61-3.969.80.085.73805639010.08100
3.96-4.439.70.05411.53436035360.054100
4.43-5.119.70.05610.73045331440.056100
5.11-6.269.60.0728.12570526790.07299.8
6.26-8.859.50.04214.11985421030.04299.6
8.85-53.3138.90.03616.11081712380.03698.3

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.20data scaling
SOLVEphasing
RESOLVEphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
MxDCdata collection
PHENIX1.8.2_1309phasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→53.31 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8301 / SU ML: 0.32 / σ(F): 1.36 / Phase error: 23.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1782 5.08 %RANDOM
Rwork0.1844 ---
all0.187 35131 --
obs0.1869 35065 99.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.57 Å2 / Biso mean: 53.4322 Å2 / Biso min: 22.23 Å2
Refine analyzeLuzzati coordinate error obs: 0.337 Å
Refinement stepCycle: LAST / Resolution: 2.8→53.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7195 0 46 45 7286
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017550
X-RAY DIFFRACTIONf_angle_d0.91410238
X-RAY DIFFRACTIONf_chiral_restr0.0661031
X-RAY DIFFRACTIONf_plane_restr0.0041360
X-RAY DIFFRACTIONf_dihedral_angle_d14.6772777
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
2.7994-2.87510.31811330.2863248826212488100
2.8751-2.95970.29011330.242255426872554100
2.9597-3.05520.30291350.2276251226472512100
3.0552-3.16440.28341250.2256254826732548100
3.1644-3.2910.30351410.2193254226832542100
3.291-3.44080.29591340.2129252526592525100
3.4408-3.62220.23111450.1875252426692524100
3.6222-3.84910.22991310.1792257427052574100
3.8491-4.14610.2081350.1636254526802545100
4.1461-4.56320.17311410.1505257827192578100
4.5632-5.2230.19651460.1517258427302584100
5.223-6.57850.22721430.1721259927422599100
6.5785-53.32210.22091400.181727102850271099

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