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- PDB-6eqi: Structure of PINK1 bound to ubiquitin -

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Basic information

Entry
Database: PDB / ID: 6eqi
TitleStructure of PINK1 bound to ubiquitin
Components
  • Nb696
  • Serine/threonine-protein kinase PINK1, putative
  • Ubiquitin
KeywordsTRANSFERASE / PINK1 Ubiquitin Mitophagy Nanobody Substrate recognition Complex Parkinson's disease
Function / homology
Function and homology information


autophagy of mitochondrion / positive regulation of mitochondrial fission / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / IRAK2 mediated activation of TAK1 complex / Prevention of phagosomal-lysosomal fusion / Alpha-protein kinase 1 signaling pathway ...autophagy of mitochondrion / positive regulation of mitochondrial fission / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / IRAK2 mediated activation of TAK1 complex / Prevention of phagosomal-lysosomal fusion / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / Regulation of FZD by ubiquitination / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / Pexophagy / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / TCF dependent signaling in response to WNT / APC/C:Cdc20 mediated degradation of Securin / Regulation of NF-kappa B signaling / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Asymmetric localization of PCP proteins / activated TAK1 mediates p38 MAPK activation / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Negative regulation of FGFR3 signaling / Deactivation of the beta-catenin transactivating complex / Fanconi Anemia Pathway / Peroxisomal protein import / Degradation of DVL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Negative regulation of FGFR2 signaling / Stabilization of p53 / Negative regulation of FGFR4 signaling / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR1 signaling / Degradation of AXIN / Regulation of TNFR1 signaling / Hh mutants are degraded by ERAD / EGFR downregulation / Activation of NF-kappaB in B cells / Termination of translesion DNA synthesis / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Degradation of GLI1 by the proteasome / G2/M Checkpoints / Hedgehog ligand biogenesis / Assembly Of The HIV Virion
Similarity search - Function
: / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily ...: / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Serine/threonine-protein kinase Pink1, mitochondrial / Polyubiquitin-C
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
Pediculus humanus corporis (human body louse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsSchubert, A.F. / Gladkova, C. / Pardon, E. / Wagstaff, J.L. / Freund, S.M.V. / Steyaert, J. / Maslen, S. / Komander, D.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)U105192732 United Kingdom
European Research Council309756
Michael J. Fox Foundation
Lister Institute for Preventive Medicine
CitationJournal: Nature / Year: 2017
Title: Structure of PINK1 in complex with its substrate ubiquitin.
Authors: Schubert, A.F. / Gladkova, C. / Pardon, E. / Wagstaff, J.L. / Freund, S.M.V. / Steyaert, J. / Maslen, S.L. / Komander, D.
History
DepositionOct 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Dec 20, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 31, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin
B: Nb696
C: Serine/threonine-protein kinase PINK1, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2656
Polymers72,9893
Non-polymers2763
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-15 kcal/mol
Surface area24290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.711, 105.711, 149.451
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Ubiquitin


Mass: 8575.804 Da / Num. of mol.: 1 / Mutation: T66V L67N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48
#2: Antibody Nb696


Mass: 14532.033 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Protein Serine/threonine-protein kinase PINK1, putative


Mass: 49880.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pediculus humanus corporis (human body louse)
Gene: 8239562, Phum_PHUM577390 / Production host: Escherichia coli (E. coli)
References: UniProt: E0W1I1, non-specific serine/threonine protein kinase
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
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: 3.54 Å3/Da / Density % sol: 62.76 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop
Details: The PhPINK1-Nb696-Ub TVLN complex was crystallised at 7 mg/ml using sitting-drop vapour diffusion against 1.3 M Ammonium Tartrate Dibasic, 0.1 M BIS-TRIS Propane pH 7.0 from a 1:1 protein to ...Details: The PhPINK1-Nb696-Ub TVLN complex was crystallised at 7 mg/ml using sitting-drop vapour diffusion against 1.3 M Ammonium Tartrate Dibasic, 0.1 M BIS-TRIS Propane pH 7.0 from a 1:1 protein to mother liquor ratio, in 100 nl drops at 295.15 K. Crystals were optimised using streak seeding with a cat whisker at 8.9 mg/ml complex concentration in 1.4 M Ammonium Tartrate, 0.1 M BIS-TRIS Propane pH 6.3 at 295.15 K.
PH range: pH 6-7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.1→49.83 Å / Num. obs: 18000 / % possible obs: 99.5 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 11.67
Reflection shellResolution: 3.1→3.31 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.18 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
Aimlessdata scaling
PHASERphasing
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q5I

3q5i


Resolution: 3.1→49.83 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.3
RfactorNum. reflection% reflection
Rfree0.2341 962 5.36 %
Rwork0.2031 --
obs0.2049 17961 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.1→49.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4426 0 18 9 4453
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044531
X-RAY DIFFRACTIONf_angle_d0.6486175
X-RAY DIFFRACTIONf_dihedral_angle_d14.8542704
X-RAY DIFFRACTIONf_chiral_restr0.043716
X-RAY DIFFRACTIONf_plane_restr0.004790
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1004-3.26380.27821390.2542390X-RAY DIFFRACTION100
3.2638-3.46830.23811370.22342408X-RAY DIFFRACTION100
3.4683-3.7360.31340.222408X-RAY DIFFRACTION100
3.736-4.11180.26691440.19932383X-RAY DIFFRACTION100
4.1118-4.70640.2111370.17572444X-RAY DIFFRACTION100
4.7064-5.9280.22061360.20352447X-RAY DIFFRACTION100
5.928-49.83730.21141350.20372519X-RAY DIFFRACTION98
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)
13.75410.0634-0.35895.08860.12924.65590.2721-0.0675-0.8580.03160.0060.32041.6898-0.4556-0.18531.2415-0.1657-0.19310.80440.08380.944345.4091-8.213123.1265
21.7495-0.67110.98492.9363-1.15463.70270.01230.0801-0.163-0.07370.1638-0.13250.1832-0.0605-0.15160.48330.03290.00090.5115-0.01710.461439.799215.0234.3828
32.9498-0.2524-0.05631.52590.07631.71620.020.2138-0.0734-0.03230.035-0.03560.05980.0246-0.05930.4806-0.0299-0.03290.4521-0.00760.46269.85047.310721.9446
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C

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