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- PDB-5n2w: WT-Parkin and pUB complex -

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Basic information

Entry
Database: PDB / ID: 5n2w
TitleWT-Parkin and pUB complex
Components
  • E3 ubiquitin-protein ligase parkin,E3 ubiquitin-protein ligase parkin
  • Polyubiquitin-B
KeywordsLIGASE / Complex structure of Parkin and pUB / Transferase
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 / negative regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway / regulation protein catabolic process at presynapse / regulation of protein targeting to mitochondrion / negative regulation of spontaneous neurotransmitter secretion / 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 / negative regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway / regulation protein catabolic process at presynapse / regulation of protein targeting to mitochondrion / negative regulation of spontaneous neurotransmitter secretion / negative regulation of intralumenal vesicle formation / negative regulation of glucokinase activity / negative regulation of exosomal secretion / mitochondrion to lysosome vesicle-mediated transport / type 2 mitophagy / Lewy body / protein K27-linked ubiquitination / Parkin-FBXW7-Cul1 ubiquitin ligase complex / negative regulation of actin filament bundle assembly / positive regulation of mitochondrial fusion / free ubiquitin chain polymerization / regulation of synaptic vesicle transport / negative regulation of mitochondrial fusion / protein K29-linked ubiquitination / : / positive regulation of protein linear polyubiquitination / RBR-type E3 ubiquitin transferase / F-box domain binding / negative regulation by host of viral genome replication / positive regulation of mitophagy / regulation of cellular response to oxidative stress / regulation of necroptotic process / regulation of dopamine metabolic process / dopaminergic synapse / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / cellular response to toxic substance / positive regulation of dendrite extension / positive regulation of tumor necrosis factor-mediated signaling pathway / protein K6-linked ubiquitination / positive regulation of proteasomal protein catabolic process / norepinephrine metabolic process / protein localization to mitochondrion / positive regulation of protein localization to membrane / negative regulation of JNK cascade / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cellular response to dopamine / mitochondrial fission / protein K11-linked ubiquitination / ubiquitin conjugating enzyme binding / aggresome assembly / regulation of mitochondrion organization / hypothalamus gonadotrophin-releasing hormone neuron development / regulation of canonical Wnt signaling pathway / aggresome / female meiosis I / positive regulation of protein monoubiquitination / regulation of reactive oxygen species metabolic process / regulation of synaptic vesicle endocytosis / mitochondrion transport along microtubule / fat pad development / autophagy of mitochondrion / positive regulation of DNA binding / positive regulation of mitochondrial fission / dopamine uptake involved in synaptic transmission / negative regulation of release of cytochrome c from mitochondria / female gonad development / regulation of dopamine secretion / seminiferous tubule development / ubiquitin-specific protease binding / startle response / male meiosis I / dopamine metabolic process / protein monoubiquitination / cullin family protein binding / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / phospholipase binding / protein K63-linked ubiquitination / regulation of protein ubiquitination / regulation of glucose metabolic process / protein deubiquitination / mitophagy / cellular response to unfolded protein / negative regulation of reactive oxygen species metabolic process / cellular response to manganese ion / protein autoubiquitination / negative regulation of insulin secretion / proteasomal protein catabolic process / protein K48-linked ubiquitination / regulation of neuron apoptotic process / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / regulation of proteasomal protein catabolic process / ubiquitin ligase complex / energy homeostasis / ERAD pathway / heat shock protein binding / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / FLT3 signaling by CBL mutants
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 ligase RBR family ...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 ligase RBR family / IBR domain / In Between Ring fingers / TRIAD supradomain / TRIAD supradomain profile. / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
trimethylamine oxide / E3 ubiquitin-protein ligase parkin / Polyubiquitin-B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsKumar, A. / Chaugule, V.K. / Johnson, C. / Toth, R. / Sundaramoorthy, R. / Knebel, A. / Walden, H.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Cancer Research UK17739 United Kingdom
Medical Research Council (United Kingdom)MC_UU_12016/12 United Kingdom
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2017
Title: Parkin-phosphoubiquitin complex reveals cryptic ubiquitin-binding site required for RBR ligase activity.
Authors: Kumar, A. / Chaugule, V.K. / Condos, T.E.C. / Barber, K.R. / Johnson, C. / Toth, R. / Sundaramoorthy, R. / Knebel, A. / Shaw, G.S. / Walden, H.
History
DepositionFeb 8, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2017Group: Database references
Revision 1.2May 17, 2017Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 31, 2018Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.5Jan 17, 2024Group: 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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_conn_type.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,E3 ubiquitin-protein ligase parkin
B: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,95013
Polymers54,2412
Non-polymers70911
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-31 kcal/mol
Surface area22550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.290, 147.290, 87.490
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 45600.023 Da / Num. of mol.: 1
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, Transferases; Acyltransferases; Aminoacyltransferases
#2: Protein Polyubiquitin-B


Mass: 8640.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Ser65 is phosphorylated to give SEP65 / Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47

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Non-polymers , 4 types, 40 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-TMO / trimethylamine oxide


Mass: 75.110 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H9NO
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.27 Å3/Da / Density % sol: 45.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 100mM Tris pH 8.5, 200mM TMAO, PEG MME 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.68→56.34 Å / Num. obs: 15028 / % possible obs: 93.6 % / Redundancy: 4.6 % / Biso Wilson estimate: 70.3 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 8.9
Reflection shellResolution: 2.68→2.81 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.719 / Mean I/σ(I) obs: 1.9 / CC1/2: 0.67 / % possible all: 93.7

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C1Z, 5CAW

5c1z

5caw


Resolution: 2.68→56.34 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.879 / SU R Cruickshank DPI: 1.966 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.329 / SU Rfree Cruickshank DPI: 0.329
RfactorNum. reflection% reflectionSelection details
Rfree0.243 758 5.05 %RANDOM
Rwork0.198 ---
obs0.201 15007 92.5 %-
Displacement parametersBiso mean: 60.35 Å2
Baniso -1Baniso -2Baniso -3
1-3.3566 Å20 Å20 Å2
2--3.3566 Å20 Å2
3----6.7132 Å2
Refine analyzeLuzzati coordinate error obs: 0.364 Å
Refinement stepCycle: 1 / Resolution: 2.68→56.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3605 0 23 29 3657
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0093720HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.145026HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1290SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes101HARMONIC2
X-RAY DIFFRACTIONt_gen_planes532HARMONIC5
X-RAY DIFFRACTIONt_it3720HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3
X-RAY DIFFRACTIONt_other_torsion20.48
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion474SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4105SEMIHARMONIC4
LS refinement shellResolution: 2.68→2.87 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3238 127 4.77 %
Rwork0.2275 2538 -
all0.2319 2665 -
obs--92.54 %
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)
12.7513-1.47391.67813.7468-1.17977.7154-0.07710.0299-0.06830.1152-0.0654-0.3332-0.00810.44210.14250.2725-0.0245-0.00160.2964-0.00340.2506-26.802-28.67927.836
24.00422.0071-0.50224.4759-0.84912.70810.111-0.5459-0.7350.4476-0.168-0.57260.44310.33140.0570.50540.0264-0.02750.35010.02540.3428-16.141-71.2120.25
31.1473-0.20260.40842.79950.20891.2394-0.02620.0391-0.0298-0.02390.0115-0.05980.23750.01820.01480.16010.02410.05360.13140.01150.01-33.937-40.79910.028
45.85940.4905-0.39119.3295-0.15488.18630.02630.64580.1488-0.52190.0561-0.6261-0.31450.5922-0.08240.4852-0.02530.17320.47050.10740.4068-26.253-12.585-5.013
59.32381.5695-0.012912.8586-3.20290.8718-0.76470.1976-0.5513-0.01760.5211-1.3288-0.00670.64450.24360.70790.0070.0650.6975-0.03390.3606-24.849-49.10417.19
63.80581.7843-0.475611.0295-1.21413.17970.08480.2959-0.27250.0293-0.1053-0.06760.21740.15870.02050.3227-0.0597-0.0050.41490.02120.2538-52.977-69.8525.412
74.1109-0.0903-0.82296.63650.03683.42940.1143-0.7349-0.13520.8127-0.2747-0.66020.12850.11920.16040.3743-0.0518-0.09970.52430.05510.1926-0.568-51.1867.018
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|1 - A|74 }
2X-RAY DIFFRACTION2{ A|82 - A|228 }
3X-RAY DIFFRACTION3{ A|229 - A|328 }
4X-RAY DIFFRACTION4{ A|329 - A|377 }
5X-RAY DIFFRACTION5{ A|387 - A|405 }
6X-RAY DIFFRACTION6{ A|413 - A|465 }
7X-RAY DIFFRACTION7{ B|1 - B|76 }

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