7MP9 | pdb_00007mp9

Crystal structure of the cytosolic domain of Tribolium castaneum PINK1 phosphorylated at Ser205 in complex with ADP analog

PDB DOI: https://doi.org/10.2210/pdb7MP9/pdb

Classification: SIGNALING PROTEIN
Organism(s): Tribolium castaneum
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2021-05-04 Released: 2021-12-01
Deposition Author(s): Rasool, S., Veyron, S., Trempe, J.F.
Funding Organization(s): Canadian Institutes of Health Research (CIHR), Natural Sciences and Engineering Research Council (NSERC, Canada), Michael J. Fox Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.306 (Depositor), 0.300 (DCC)
R-Value Work:
0.247 (Depositor), 0.246 (DCC)
R-Value Observed:
0.250 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Mechanism of PINK1 activation by autophosphorylation and insights into assembly on the TOM complex.

Rasool, S., Veyron, S., Soya, N., Eldeeb, M.A., Lukacs, G.L., Fon, E.A., Trempe, J.F.

(2022) Mol Cell 82: 44

PubMed: 34875213 Search on PubMed
DOI: https://doi.org/10.1016/j.molcel.2021.11.012
Primary Citation Related Structures:
7MP8, 7MP9

PubMed Abstract:
Mutations in PINK1 cause autosomal-recessive Parkinson's disease. Mitochondrial damage results in PINK1 import arrest on the translocase of the outer mitochondrial membrane (TOM) complex, resulting in the activation of its ubiquitin kinase activity by autophosphorylation and initiation of Parkin-dependent mitochondrial clearance. Herein, we report crystal structures of the entire cytosolic domain of insect PINK1. Our structures reveal a dimeric autophosphorylation complex targeting phosphorylation at the invariant Ser205 (human Ser228). The dimer interface requires insert 2, which is unique to PINK1. The structures also reveal how an N-terminal helix binds to the C-terminal extension and provide insights into stabilization of PINK1 on the core TOM complex.

Organizational Affiliation

Department of Pharmacology & Therapeutics and Centre de Recherche en Biologie Structurale, McGill University, Montréal, QC, Canada.

Macromolecule Content

Total Structure Weight: 52.69 kDa
Atom Count: 3,335
Modeled Residue Count: 414
Deposited Residue Count: 455
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase PINK1, mitochondrial-like Protein	A	455	Tribolium castaneum	Mutation(s): 0 Gene Names: TcasGA2_TC013202 EC: 2.7.11.1
UniProt
Find proteins for D6WMX4 (Tribolium castaneum) Explore D6WMX4 Go to UniProtKB: D6WMX4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D6WMX4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AN2 Query on AN2 Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	AMP PHOSPHORAMIDATE C₁₀ H₁₆ N₆ O₉ P₂ FQMDCEJHLOLKLI-KQYNXXCUSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	G [auth A], H [auth A], I [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	C [auth A], D [auth A], E [auth A], F [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP Query on SEP	A	L-PEPTIDE LINKING	C₃ H₈ N O₆ P		SER
TPO Query on TPO	A	L-PEPTIDE LINKING	C₄ H₁₀ N O₆ P		THR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.306 (Depositor), 0.300 (DCC)
R-Value Work: 0.247 (Depositor), 0.246 (DCC)
R-Value Observed: 0.250 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.736	α = 90
b = 52.736	β = 90
c = 547.944	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
STARANISO	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-12-01

Deposition Author(s):

Rasool, S.

Veyron, S.

Trempe, J.F.

Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	153274
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	06497-2015
Michael J. Fox Foundation	Canada	12119