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- EMDB-42806: Structure of AMP-PNP-bound Pediculus humanus (Ph) PINK1 dimer -

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Basic information

Entry
Database: EMDB / ID: EMD-42806
TitleStructure of AMP-PNP-bound Pediculus humanus (Ph) PINK1 dimer
Map dataMap (sharpened) of the AMP-PNP-bound PhPINK1 dimer
Sample
  • Complex: AMP-PNP-bound Pediculus humanus (Ph) PINK1 dodecamer
    • Protein or peptide: Serine/threonine-protein kinase Pink1, mitochondrial
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
KeywordsPINK1 / Kinase / Mitophagy / Parkinson's Disease / Ubiquitin / Phosphorylation / Phospho-ubiquitin / TRANSFERASE
Function / homology
Function and homology information


autophagy of mitochondrion / positive regulation of mitochondrial fission / regulation of apoptotic process / mitochondrial outer membrane / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity ...autophagy of mitochondrion / positive regulation of mitochondrial fission / regulation of apoptotic process / mitochondrial outer membrane / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / mitochondrial inner membrane / non-specific serine/threonine protein kinase / protein kinase activity / ATP binding / metal ion binding / cytosol
Similarity search - Function
: / 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
Similarity search - Component
Biological speciesPediculus humanus corporis (human body louse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsGan ZY / Kirk NS / Leis A / Komander D
Funding support Australia, United States, 2 items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
Michael J. Fox Foundation United States
CitationJournal: 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
DepositionNov 13, 2023-
Header (metadata) releaseJan 31, 2024-
Map releaseJan 31, 2024-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42806.png

Downloads & links

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Map

FileDownload / File: emd_42806.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap (sharpened) of the AMP-PNP-bound PhPINK1 dimer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 256 pix.
= 206.848 Å		0.81 Å/pix.
x 256 pix.
= 206.848 Å		0.81 Å/pix.
x 256 pix.
= 206.848 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.808 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.55783373 - 0.82407784
Average (Standard dev.)0.0010152869 (±0.02467081)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 206.848 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map of the AMP-PNP-bound PhPINK1 dimer

Fileemd_42806_half_map_1.map
AnnotationHalf map of the AMP-PNP-bound PhPINK1 dimer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of the AMP-PNP-bound PhPINK1 dimer

Fileemd_42806_half_map_2.map
AnnotationHalf map of the AMP-PNP-bound PhPINK1 dimer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : AMP-PNP-bound Pediculus humanus (Ph) PINK1 dodecamer

EntireName: AMP-PNP-bound Pediculus humanus (Ph) PINK1 dodecamer
Components
  • Complex: AMP-PNP-bound Pediculus humanus (Ph) PINK1 dodecamer
    • Protein or peptide: Serine/threonine-protein kinase Pink1, mitochondrial
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION

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Supramolecule #1: AMP-PNP-bound Pediculus humanus (Ph) PINK1 dodecamer

SupramoleculeName: AMP-PNP-bound Pediculus humanus (Ph) PINK1 dodecamer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Pediculus humanus corporis (human body louse)

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Macromolecule #1: Serine/threonine-protein kinase Pink1, mitochondrial

MacromoleculeName: Serine/threonine-protein kinase Pink1, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pediculus humanus corporis (human body louse)
Molecular weightTheoretical: 53.053602 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #2: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 2 / Number of copies: 2 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 3 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.9 mg/mL
BufferpH: 8.5
Component:
ConcentrationNameFormula
25.0 mMtrisaminomethane
150.0 mMsodium chlorideNaCl
10.0 mMdithiothreitol
10.0 mMmagnesium chlorideMgCl2
10.0 mMadenylyl-imidodiphosphate
GridModel: 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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 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

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 114790
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7t4n


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL
Output model

PDB-8uyh:
Structure of AMP-PNP-bound Pediculus humanus (Ph) PINK1 dimer

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