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- PDB-4bm9: Structure of the autoinhibited Parkin catalytic domain -

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Basic information

Entry
Database: PDB / ID: 4bm9
TitleStructure of the autoinhibited Parkin catalytic domain
ComponentsE3 UBIQUITIN-PROTEIN LIGASE PARKIN
KeywordsLIGASE / NEURODEGENERATIVE DISEASE
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 / negative regulation of exosomal secretion / mitochondrion to lysosome vesicle-mediated transport / 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 / protein K6-linked ubiquitination / positive regulation of dendrite extension / 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 / ERAD pathway / protein monoubiquitination / phospholipase binding / cullin family protein binding / protein K63-linked ubiquitination / mitophagy / regulation of protein ubiquitination / regulation of glucose metabolic process / negative regulation of insulin secretion / negative regulation of reactive oxygen species metabolic process / cellular response to unfolded protein / positive regulation of DNA binding / cellular response to manganese ion / protein autoubiquitination / protein K48-linked ubiquitination / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / ubiquitin ligase complex / Hsp70 protein binding / heat shock protein binding / PINK1-PRKN Mediated Mitophagy / response to endoplasmic reticulum stress / mitochondrion organization / tubulin binding / adult locomotory behavior / proteasomal protein catabolic process / Josephin domain DUBs / regulation of mitochondrial membrane potential / negative regulation of protein phosphorylation / ubiquitin binding / learning / central nervous system development / synaptic transmission, glutamatergic / regulation of autophagy / 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 / SYNCHROTRON / SAD / Resolution: 2.25 Å
AuthorsWauer, T. / Komander, D.
CitationJournal: Embo J. / Year: 2013
Title: Structure of the Human Parkin Ligase Domain in an Autoinhibited State.
Authors: Wauer, T. / Komander, D.
History
DepositionMay 7, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2013Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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_asym_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_conn.ptnr2_label_seq_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

Downloads & links

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Assembly

Deposited unit
A: E3 UBIQUITIN-PROTEIN LIGASE PARKIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,72513
Polymers36,8211
Non-polymers90412
Water1,56787
1
A: E3 UBIQUITIN-PROTEIN LIGASE PARKIN
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)226,34878
Polymers220,9266
Non-polymers5,42172
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation6_556-x,-x+y,-z+11
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation5_556x-y,-y,-z+11
Buried area18930 Å2
ΔGint-586.4 kcal/mol
Surface area83320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.420, 168.420, 97.181
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-1475-

SO4

21A-2039-

HOH

31A-2082-

HOH

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Components

#1: Protein E3 UBIQUITIN-PROTEIN LIGASE PARKIN / PARKINSON JUVENILE DISEASE PROTEIN 2 / PARKINSON DISEASE PROTEIN 2 / PARKIN


Mass: 36821.051 Da / Num. of mol.: 1 / Fragment: UPD AND RBR DOMAIN, RESIDUES 137-465
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2
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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / 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.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 87 / 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 Å3/Da / Density % sol: 58.8 % / Description: NONE
Crystal growpH: 7
Details: 1.6 M LITHIUM SULPHATE, 10 MM MAGNESIUM CHLORIDE, 50 MM MES (PH 5.4)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1
DetectorType: DECTRIS PIXEL / Detector: PIXEL / Date: Feb 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→58.33 Å / Num. obs: 24502 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Biso Wilson estimate: 42.75 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.3
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 5 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.3 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.25→48.619 Å / SU ML: 0.21 / σ(F): 1.34 / Phase error: 23.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2178 1246 5.1 %
Rwork0.1903 --
obs0.1918 24502 97.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→48.619 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2279 0 29 87 2395
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062361
X-RAY DIFFRACTIONf_angle_d0.9743212
X-RAY DIFFRACTIONf_dihedral_angle_d16.629832
X-RAY DIFFRACTIONf_chiral_restr0.066344
X-RAY DIFFRACTIONf_plane_restr0.005418
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2501-2.34010.30161510.26962591X-RAY DIFFRACTION99
2.3401-2.44660.25561470.23852571X-RAY DIFFRACTION99
2.4466-2.57560.23481500.22672598X-RAY DIFFRACTION99
2.5756-2.7370.27781280.21832586X-RAY DIFFRACTION98
2.737-2.94830.25691340.22242605X-RAY DIFFRACTION98
2.9483-3.24490.23381260.20422600X-RAY DIFFRACTION98
3.2449-3.71430.20631270.17732560X-RAY DIFFRACTION97
3.7143-4.67910.17491470.15422577X-RAY DIFFRACTION96
4.6791-48.630.2081360.18112568X-RAY DIFFRACTION94
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.6699-0.23650.621.8064-1.0273.5802-0.10870.03740.48230.05190.01420.1748-0.1695-0.08590.0990.1429-0.02740.05320.16070.06890.3154-4.685237.828340.8627
25.30740.5771-0.85663.2795-0.03692.7110.0540.6927-0.3486-0.1163-0.0830.0320.0795-0.0718-0.00990.14460.02930.0220.2570.00670.153117.507329.490332.7026
31.75330.8209-0.60555.1590.5431.35740.3375-0.1642-0.19341.276-0.9036-1.77780.06280.38150.18830.8087-0.1976-0.12880.42650.09650.56137.26337.59841.5675
40.10970.07390.62315.39140.12016.52-0.03010.2973-0.2044-0.4234-0.07750.28690.4769-0.29010.30010.4545-0.0458-0.04530.478-0.22190.901813.620114.240127.2699
53.92382.66150.12172.8388-0.05451.456-0.34990.57190.1755-0.61030.23440.17790.0441-0.05140.10770.3042-0.05680.00750.22240.09410.2854-17.265422.961636.8067
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 142 THROUGH 227 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 228 THROUGH 327 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 328 THROUGH 382 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 391 THROUGH 404 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 414 THROUGH 465 )

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