[English] 日本語
Yorodumi
- EMDB-25680: Structure of dodecameric unphosphorylated Pediculus humanus (Ph) ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-25680
TitleStructure of dodecameric unphosphorylated Pediculus humanus (Ph) PINK1 D357A mutant
Map dataDodecamer map (locally filtered)
Sample
  • Complex: Dodecameric unphosphorylated Pediculus humanus (Ph) PINK1 D357A mutant
    • Protein or peptide: Serine/threonine-protein kinase PINK1, putative
KeywordsPINK1 / Kinase / Transferase / Mitophagy / Parkinson's Disease / Ubiquitin / Phosphorylation / Phospho-ubiquitin
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: 2.48 Å
AuthorsGan ZY / Leis A
Funding support United States, 2 items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) United States
Michael J. Fox Foundation United States
CitationJournal: 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
DepositionDec 10, 2021-
Header (metadata) releaseJan 12, 2022-
Map releaseJan 12, 2022-
UpdateFeb 28, 2024-
Current statusFeb 28, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7t4m
  • Surface level: 0.2
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7t4m
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_25680.png

Downloads & links

-
Map

FileDownload / File: emd_25680.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDodecamer map (locally filtered)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 380 pix.
= 316.54 Å		0.83 Å/pix.
x 380 pix.
= 316.54 Å		0.83 Å/pix.
x 380 pix.
= 316.54 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.833 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2 / Movie #1: 0.2
Minimum - Maximum-0.35183662 - 0.68646544
Average (Standard dev.)0.00023379482 (±0.024600733)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 316.54 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8330.8330.833
M x/y/z380380380
origin x/y/z0.0000.0000.000
length x/y/z316.540316.540316.540
α/β/γ90.00090.00090.000
start NX/NY/NZ253841
NX/NY/NZ999350
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS380380380
D min/max/mean-0.8051.2520.002

-
Supplemental data

-
Mask #1

Fileemd_25680_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Dodecamer map (unsharpened)

Fileemd_25680_additional_1.map
AnnotationDodecamer map (unsharpened)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Dodecamer half map

Fileemd_25680_half_map_1.map
AnnotationDodecamer half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Dodecamer half map

Fileemd_25680_half_map_2.map
AnnotationDodecamer half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Dodecameric unphosphorylated Pediculus humanus (Ph) PINK1 D357A mutant

EntireName: Dodecameric unphosphorylated Pediculus humanus (Ph) PINK1 D357A mutant
Components
  • Complex: Dodecameric unphosphorylated Pediculus humanus (Ph) PINK1 D357A mutant
    • Protein or peptide: Serine/threonine-protein kinase PINK1, putative

-
Supramolecule #1: Dodecameric unphosphorylated Pediculus humanus (Ph) PINK1 D357A mutant

SupramoleculeName: Dodecameric unphosphorylated Pediculus humanus (Ph) PINK1 D357A mutant
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pediculus humanus corporis (human body louse)
Molecular weightTheoretical: 604 KDa

-
Macromolecule #1: Serine/threonine-protein kinase PINK1, putative

MacromoleculeName: Serine/threonine-protein kinase PINK1, putative / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Pediculus humanus corporis (human body louse)
Molecular weightTheoretical: 52.929613 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 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

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2 mg/mL
BufferpH: 8.5
Component:
ConcentrationFormulaName
25.0 mMTristrisaminomethane
150.0 mMNaClsodium chloride
10.0 mMDTTdithiothreitol
GridModel: 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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Slit width: 10 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.25 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: 1.9000000000000001 µm / Nominal defocus min: 0.4 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.48 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 216021
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2.0)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

6eqi


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

PDB-7t4m:
Structure of dodecameric unphosphorylated Pediculus humanus (Ph) PINK1 D357A mutant

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more