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- PDB-5n38: S65DParkin and pUB complex -

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Basic information

Entry
Database: PDB / ID: 5n38
TitleS65DParkin and pUB complex
Components
  • E3 ubiquitin-protein ligase parkin,E3 ubiquitin-protein ligase parkin
  • Polyubiquitin-B
KeywordsLIGASE / S65DParkin pUB complex / splicing
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 / 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 ...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 / 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 / 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 / negative regulation of excitatory postsynaptic potential / cellular response to L-glutamate / autophagy of mitochondrion / dopaminergic synapse / mitochondrion localization / aggresome / protein localization to mitochondrion / mitochondrial fission / cellular response to dopamine / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / cellular response to toxic substance / positive regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / positive regulation of protein localization to membrane / regulation of mitochondrion organization / protein K11-linked ubiquitination / negative regulation of reactive oxygen species metabolic process / protein K6-linked ubiquitination / neuron cellular homeostasis / positive regulation of proteasomal protein catabolic process / negative regulation of JNK cascade / negative regulation of synaptic transmission, glutamatergic / ubiquitin conjugating enzyme binding / regulation of reactive oxygen species metabolic process / mitochondrion transport along microtubule / positive regulation of mitochondrial membrane potential / regulation of canonical Wnt signaling pathway / positive regulation of protein monoubiquitination / 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 / dopamine metabolic process / ubiquitin-specific protease binding / Lewy body / regulation of glucose metabolic process / regulation of dopamine secretion / positive regulation of ATP biosynthetic process / cellular response to unfolded protein / regulation of protein ubiquitination / negative regulation of insulin secretion / protein monoubiquitination / cullin family protein binding / regulation of synaptic vesicle endocytosis / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of mitochondrial fission / protein deubiquitination / mitophagy / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / ubiquitin ligase complex / regulation of postsynaptic membrane neurotransmitter receptor levels / adult locomotory behavior / protein K63-linked ubiquitination / protein autoubiquitination / negative regulation of reactive oxygen species biosynthetic process / phospholipase binding / cellular response to manganese ion / heat shock protein binding / ERAD pathway / protein K48-linked ubiquitination / neuron projection morphogenesis / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / regulation of neuron apoptotic process
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. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / E3 ubiquitin-protein ligase parkin / Polyubiquitin-B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 1.4Feb 7, 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 / pdbx_struct_special_symmetry / 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
Revision 1.6Nov 13, 2024Group: Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _struct_conn.pdbx_leaving_atom_flag

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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)54,93412
Polymers54,2692
Non-polymers66510
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-30 kcal/mol
Surface area22970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.540, 146.540, 88.440
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-2638-

HOH

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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: 45628.035 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 / 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, 65 molecules

#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.53 Å3/Da / Density % sol: 51.3 %
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: I04 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.6→72.56 Å / Num. obs: 17000 / % possible obs: 96.4 % / Redundancy: 3.5 % / Biso Wilson estimate: 63.57 Å2 / Net I/σ(I): 9.1
Reflection shellResolution: 2.6→2.76 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.2 / CC1/2: 0.64 / % possible all: 88.4

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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: 2.6→72.56 Å / Cor.coef. Fo:Fc: 0.9357 / Cor.coef. Fo:Fc free: 0.9141 / SU R Cruickshank DPI: 0.595 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.686 / SU Rfree Blow DPI: 0.288 / SU Rfree Cruickshank DPI: 0.286
RfactorNum. reflection% reflectionSelection details
Rfree0.236 874 5.15 %RANDOM
Rwork0.1865 ---
obs0.1891 16984 95.81 %-
Displacement parametersBiso mean: 53.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.8256 Å20 Å20 Å2
2--0.8256 Å20 Å2
3----1.6513 Å2
Refine analyzeLuzzati coordinate error obs: 0.347 Å
Refinement stepCycle: 1 / Resolution: 2.6→72.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3552 0 13 55 3620
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013645HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.224929HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1258SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes98HARMONIC2
X-RAY DIFFRACTIONt_gen_planes524HARMONIC5
X-RAY DIFFRACTIONt_it3645HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.22
X-RAY DIFFRACTIONt_other_torsion21.81
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion466SEMIHARMONIC5
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_contact3987SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.76 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.3082 136 5.53 %
Rwork0.2228 2323 -
all0.2275 2459 -
obs--95.81 %
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)
12.1022-0.25731.24722.6719-0.11485.5070.0846-0.2468-0.02410.03620.0467-0.25820.29950.3226-0.1313-0.04030.0166-0.0135-0.04760.0199-0.07-26.1996-28.453828.1842
22.47820.5296-0.32272.5890.98641.60070.2216-0.4305-0.35020.3628-0.0802-0.4820.44490.0521-0.14140.0256-0.0689-0.0841-0.13150.0454-0.0311-16.1321-71.1289-0.7945
30.8637-0.2553-0.09931.9115-0.47951.0956-0.0582-0.0746-0.0398-0.04370.0046-0.00350.18980.06130.05360.01370.01440.0433-0.04060.0132-0.0623-33.5039-40.195510.2082
40.57930.58871.08816.6209-0.05515.4814-0.00630.24880.0682-0.30630.1002-0.1909-0.24060.0506-0.09390.04040.01640.1031-0.05410.112-0.0448-26.3489-12.0189-5.4347
52.0431-0.9263-1.8681-0.13340.04180.7507-0.02560.0234-0.19610.0596-0.077-0.02650.04080.10890.10260.10820.03060.1253-0.07870.0869-0.0127-26.4093-55.240217.2841
61.03460.6656-1.26916.7811-0.43882.37440.00960.0040.1905-0.086-0.08510.2888-0.20580.19010.0755-0.0277-0.0571-0.0086-0.00780.0024-0.0739-52.555-69.10415.9718
72.7166-0.1149-0.29664.4110.012.12840.0344-0.5416-0.33880.54690.0314-0.21840.27010.0258-0.0658-0.01570.0008-0.07290.05220.055-0.1385-0.3978-51.46296.7824
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|1-74 }
2X-RAY DIFFRACTION2{ A|79-228 }
3X-RAY DIFFRACTION3{ A|229-328 }
4X-RAY DIFFRACTION4{ A|329-377 }
5X-RAY DIFFRACTION5{ A|393-405 }
6X-RAY DIFFRACTION6{ A|413-465 }
7X-RAY DIFFRACTION7{ B|* }

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