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Yorodumi- EMDB-25681: Structure of dimeric unphosphorylated Pediculus humanus (Ph) PINK... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25681 | |||||||||
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Title | Structure of dimeric unphosphorylated Pediculus humanus (Ph) PINK1 D357A mutant | |||||||||
Map data | Dimer map (locally filtered). Generated from local refinement of a dimer from the dodecamer (EMD-25680). | |||||||||
Sample |
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Keywords | PINK1 / Kinase / Transferase / Mitophagy / Parkinson's Disease / Ubiquitin / Phosphorylation / Phospho-ubiquitin | |||||||||
Function / homology | Function and homology information positive regulation of mitochondrial fission / autophagy / regulation of apoptotic process / mitochondrial outer membrane / non-specific serine/threonine protein kinase / mitochondrial inner membrane / 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: 2.35 Å | |||||||||
Authors | Gan ZY / Leis A | |||||||||
Funding support | Australia, United States, 2 items
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Citation | Journal: Nature / Year: 2022 Title: Activation mechanism of PINK1. Authors: Zhong Yan Gan / Sylvie Callegari / Simon A Cobbold / Thomas R Cotton / Michael J Mlodzianoski / Alexander F Schubert / Niall D Geoghegan / Kelly L Rogers / Andrew Leis / Grant Dewson / Alisa ...Authors: Zhong Yan Gan / Sylvie Callegari / Simon A Cobbold / Thomas R Cotton / Michael J Mlodzianoski / Alexander F Schubert / Niall D Geoghegan / Kelly L Rogers / Andrew Leis / Grant Dewson / Alisa Glukhova / David Komander / Abstract: Mutations in the protein kinase PINK1 lead to defects in mitophagy and cause autosomal recessive early onset Parkinson's disease. PINK1 has many unique features that enable it to phosphorylate ...Mutations in the protein kinase PINK1 lead to defects in mitophagy and cause autosomal recessive early onset Parkinson's disease. PINK1 has many unique features that enable it to phosphorylate ubiquitin and the ubiquitin-like domain of Parkin. Structural analysis of PINK1 from diverse insect species with and without ubiquitin provided snapshots of distinct structural states yet did not explain how PINK1 is activated. Here we elucidate the activation mechanism of PINK1 using crystallography and cryo-electron microscopy (cryo-EM). A crystal structure of unphosphorylated Pediculus humanus corporis (Ph; human body louse) PINK1 resolves an N-terminal helix, revealing the orientation of unphosphorylated yet active PINK1 on the mitochondria. We further provide a cryo-EM structure of a symmetric PhPINK1 dimer trapped during the process of trans-autophosphorylation, as well as a cryo-EM structure of phosphorylated PhPINK1 undergoing a conformational change to an active ubiquitin kinase state. Structures and phosphorylation studies further identify a role for regulatory PINK1 oxidation. Together, our research delineates the complete activation mechanism of PINK1, illuminates how PINK1 interacts with the mitochondrial outer membrane and reveals how PINK1 activity may be modulated by mitochondrial reactive oxygen species. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_25681.map.gz | 2.4 MB | EMDB map data format | |
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Header (meta data) | emd-25681-v30.xml emd-25681.xml | 19.7 KB 19.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_25681_fsc.xml | 14.1 KB | Display | FSC data file |
Images | emd_25681.png | 76 KB | ||
Masks | emd_25681_msk_1.map | 209.3 MB | Mask map | |
Filedesc metadata | emd-25681.cif.gz | 6.2 KB | ||
Others | emd_25681_additional_1.map.gz emd_25681_half_map_1.map.gz emd_25681_half_map_2.map.gz | 105.4 MB 194 MB 194 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25681 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25681 | HTTPS FTP |
-Validation report
Summary document | emd_25681_validation.pdf.gz | 868.7 KB | Display | EMDB validaton report |
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Full document | emd_25681_full_validation.pdf.gz | 868.3 KB | Display | |
Data in XML | emd_25681_validation.xml.gz | 21.3 KB | Display | |
Data in CIF | emd_25681_validation.cif.gz | 27.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25681 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25681 | HTTPS FTP |
-Related structure data
Related structure data | 7t4nMC 7t3xC 7t4kC 7t4lC 7t4mC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_25681.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Dimer map (locally filtered). Generated from local refinement of a dimer from the dodecamer (EMD-25680). | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.833 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_25681_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Dimer map (unsharpened)
File | emd_25681_additional_1.map | ||||||||||||
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Annotation | Dimer map (unsharpened) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Dimer half map
File | emd_25681_half_map_1.map | ||||||||||||
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Annotation | Dimer half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Dimer half map
File | emd_25681_half_map_2.map | ||||||||||||
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Annotation | Dimer half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Dodecameric unphosphorylated Pediculus humanus (Ph) PINK1 D357A mutant
Entire | Name: Dodecameric unphosphorylated Pediculus humanus (Ph) PINK1 D357A mutant |
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Components |
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-Supramolecule #1: Dodecameric unphosphorylated Pediculus humanus (Ph) PINK1 D357A mutant
Supramolecule | Name: Dodecameric unphosphorylated Pediculus humanus (Ph) PINK1 D357A mutant type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Pediculus humanus corporis (human body louse) |
Molecular weight | Theoretical: 604 KDa |
-Macromolecule #1: Serine/threonine-protein kinase PINK1, putative
Macromolecule | Name: Serine/threonine-protein kinase PINK1, putative / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase |
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Source (natural) | Organism: Pediculus humanus corporis (human body louse) |
Molecular weight | Theoretical: 52.929613 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 LRDKTPNMRS SILLLSQLLE AVAHMNIHNI SHRDLKSDNI LVDLSEGDAY PT IVITAFG CCLCDKQNGL VIPYRSEDQD KGGNRALMAP EIANAKPGTF SWLNYKKSDL WAVGAIAYEI FNIDNPFYDK TMK LLSKSY KEEDLPELPD TIPFIIRNLV SNMLSRSTNK RLDCDVAATV AQLYLWAPSS WLKENYTLPN SNEIIQWLLC LSSK VLCER DITARNKTNT MSESVSKAQY KGRRSLPEYE LIASFLRRVR LHLVRKGLKW IQELHIYN UniProtKB: Serine/threonine-protein kinase Pink1, mitochondrial |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 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 - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 0.039 kPa | ||||||||||||
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: 10 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.25 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: 1.9000000000000001 µm / Nominal defocus min: 0.4 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |