+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-42806 | |||||||||
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Title | Structure of AMP-PNP-bound Pediculus humanus (Ph) PINK1 dimer | |||||||||
Map data | Map (sharpened) of the AMP-PNP-bound PhPINK1 dimer | |||||||||
Sample |
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Keywords | PINK1 / Kinase / Mitophagy / Parkinson's Disease / Ubiquitin / Phosphorylation / Phospho-ubiquitin / TRANSFERASE | |||||||||
Function / homology | Function and homology information positive regulation of mitochondrial fission / autophagy / regulation of apoptotic process / mitochondrial outer membrane / mitochondrial inner membrane / non-specific serine/threonine protein kinase / protein kinase activity / protein serine/threonine kinase activity / ATP binding / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Pediculus humanus corporis (human body louse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.84 Å | |||||||||
Authors | Gan ZY / Kirk NS / Leis A / Komander D | |||||||||
Funding support | Australia, United States, 2 items
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Citation | Journal: Sci Adv / Year: 2024 Title: Interaction of PINK1 with nucleotides and kinetin. Authors: Zhong Yan Gan / Sylvie Callegari / Thanh N Nguyen / Nicholas S Kirk / Andrew Leis / Michael Lazarou / Grant Dewson / David Komander / Abstract: The ubiquitin kinase PINK1 accumulates on damaged mitochondria to trigger mitophagy, and PINK1 loss-of-function mutations cause early onset Parkinson's disease. Nucleotide analogs such as kinetin ...The ubiquitin kinase PINK1 accumulates on damaged mitochondria to trigger mitophagy, and PINK1 loss-of-function mutations cause early onset Parkinson's disease. Nucleotide analogs such as kinetin triphosphate (KTP) were reported to enhance PINK1 activity and may represent a therapeutic strategy for the treatment of Parkinson's disease. Here, we investigate the interaction of PINK1 with nucleotides, including KTP. We establish a cryo-EM platform exploiting the dodecamer assembly of () PINK1 and determine PINK1 structures bound to AMP-PNP and ADP, revealing conformational changes in the kinase N-lobe that help establish PINK1's ubiquitin binding site. Notably, we find that KTP is unable to bind PINK1 or human () PINK1 due to a steric clash with the kinase "gatekeeper" methionine residue, and mutation to Ala or Gly is required for PINK1 to bind and use KTP as a phosphate donor in ubiquitin phosphorylation and mitophagy. PINK1 M318G can be used to conditionally uncouple PINK1 stabilization and activity on mitochondria. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_42806.map.gz | 59.7 MB | EMDB map data format | |
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Header (meta data) | emd-42806-v30.xml emd-42806.xml | 18.7 KB 18.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_42806_fsc.xml | 8.4 KB | Display | FSC data file |
Images | emd_42806.png | 86.8 KB | ||
Filedesc metadata | emd-42806.cif.gz | 6.3 KB | ||
Others | emd_42806_half_map_1.map.gz emd_42806_half_map_2.map.gz | 59.4 MB 59.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-42806 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-42806 | HTTPS FTP |
-Validation report
Summary document | emd_42806_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_42806_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_42806_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | emd_42806_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42806 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42806 | HTTPS FTP |
-Related structure data
Related structure data | 8uyhMC 8uyfC 8uyiC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_42806.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Map (sharpened) of the AMP-PNP-bound PhPINK1 dimer | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.808 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half map of the AMP-PNP-bound PhPINK1 dimer
File | emd_42806_half_map_1.map | ||||||||||||
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Annotation | Half map of the AMP-PNP-bound PhPINK1 dimer | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map of the AMP-PNP-bound PhPINK1 dimer
File | emd_42806_half_map_2.map | ||||||||||||
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Annotation | Half map of the AMP-PNP-bound PhPINK1 dimer | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : AMP-PNP-bound Pediculus humanus (Ph) PINK1 dodecamer
Entire | Name: AMP-PNP-bound Pediculus humanus (Ph) PINK1 dodecamer |
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Components |
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-Supramolecule #1: AMP-PNP-bound Pediculus humanus (Ph) PINK1 dodecamer
Supramolecule | Name: AMP-PNP-bound Pediculus humanus (Ph) PINK1 dodecamer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Pediculus humanus corporis (human body louse) |
-Macromolecule #1: Serine/threonine-protein kinase Pink1, mitochondrial
Macromolecule | Name: Serine/threonine-protein kinase Pink1, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Pediculus humanus corporis (human body louse) |
Molecular weight | Theoretical: 53.053602 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GPSGLLTKDD ELEGICWEIR EAVSKGKWND SESENVEQLQ AANLDELDLG EPIAKGCNAV VYSAKLKNVQ SNKLAHQLAV KMMFNYDVE SNSTAILKAM YRETVPAMSY FFNQNLFNIE NISDFKIRLP PHPNIVRMYS VFADRIPDLQ CNKQLYPEAL P PRINPEGS ...String: GPSGLLTKDD ELEGICWEIR EAVSKGKWND SESENVEQLQ AANLDELDLG EPIAKGCNAV VYSAKLKNVQ SNKLAHQLAV KMMFNYDVE SNSTAILKAM YRETVPAMSY FFNQNLFNIE NISDFKIRLP PHPNIVRMYS VFADRIPDLQ CNKQLYPEAL P PRINPEGS GRNMSLFLVM KRYDCTLKEY LRDK(TPO)PNMRS SILLLSQLLE AVAHMNIHNI SHRDLKSDNI LVDLSEGD A YPTIVITDFG CCLCDKQNGL VIPYRSEDQD KGGNRALMAP EIANAKPGTF SWLNYKKSDL WAVGAIAYEI FNIDNPFYD KTMKLLSKSY KEEDLPELPD TIPFIIRNLV SNMLSRSTNK RLDCDVAATV AQLYLWAPSS WLKENYTLPN SNEIIQWLLC LSSKVLCER DITARNKTNT MSESVSKAQY KGRRSLPEYE LIASFLRRVR LHLVRKGLKW IQELHIYN UniProtKB: Serine/threonine-protein kinase Pink1, mitochondrial |
-Macromolecule #2: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Macromolecule | Name: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 2 / Number of copies: 2 / Formula: ANP |
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Molecular weight | Theoretical: 506.196 Da |
Chemical component information | ChemComp-ANP: |
-Macromolecule #3: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 3 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.9 mg/mL | ||||||||||||||||||
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Buffer | pH: 8.5 Component:
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Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |