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Catalog
ASAP is committed to accelerating the pace of discovery and informing a path to a cure for Parkinson’s disease through collaboration, research-enabling resources, and data sharing. We’ve created this catalog to showcase the research outputs and tools developed by ASAP-funded programs.
Dataset
Crystal structure ATG9 HDIR in complex with the ATG13:ATG101 HORMA dimer
Experimental Data Snapshot
Crystal structure ATG9 HDIR in complex with the ATG13:ATG101 HORMA dimer
PDB DOI: 10.2210/pdb8DO8/pdb
Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No
Deposited: 2022-07-12 Released: 2022-11-23
Deposition Author(s): Buffalo, C.Z., Ren, X., Yokom, A.L., Hurley, J.H.
Funding Organization(s): Other private
Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free: 0.251
R-Value Work: 0.204
R-Value Observed: 0.205
Teams
Themes
Dataset
Structure of human ULK1 complex core (2:2:2 stoichiometry) in the PI3KC3-C1 mixture
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No
Deposited: 2023-05-04
Released: 2023-06-21
Deposition Author(s): Chen, M., Hurley, J.H.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Michael J. Fox Foundation
Teams
Themes
Dataset
Structure of human ULK1C:PI3KC3-C1 supercomplex
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No
Deposited: 2023-05-05
Released: 2023-06-21
Deposition Author(s): Chen, M., Hurley, J.H.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Michael J. Fox Foundation
Teams
Themes
Dataset
Structure of human PI3KC3-C1 complex
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No
Deposited: 2023-04-29
Released: 2023-06-21
Deposition Author(s): Chen, M., Hurley, J.H.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Michael J. Fox Foundation
Teams
Themes
Dataset
Structure of human ULK1 complex core (2:1:1 stoichiometry)
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No
Deposited: 2023-04-28
Released: 2023-06-21
Deposition Author(s): Chen, M., Hurley, J.H.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Michael J. Fox Foundation
Teams
Themes
Dataset
Structure of human ULK1 complex core (2:2:2 stoichiometry) of the ATG13(450-517) mutant
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No
Deposited: 2023-05-05
Released: 2023-06-21
Deposition Author(s): Chen, M., Hurley, J.H.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Michael J. Fox Foundation
Teams
Themes
Article
In situ structural analysis reveals membrane shape transitions during autophagosome formation
Preprint: A hallmark of PD is the failure of quality control mechanisms in the cell, such as autophagy. The authors combined cell biology with correlative cryo-electron tomography in yeast cells to show a high resolution stepwise structural progression of autophagosome biogenesis. Further, they revealed the organelle interactome for growing autophagosomes.
Themes
Protocol
Halo-LC3B processing assay to assess autophagy
This protocol details Halo-LC3B processing assay to assess autophagy.
Teams
Themes
Protocol
RNA extraction and quantitative PCR to assay inflammatory gene expression
The authors developed this protocol to test levels of NF-kB response genes in a cell model transiently over-expressing Parkin. With this technique the authors found significant upregulation of key pro-inflammatory genes normalized to a housekeeping gene, Gapdh.
Teams
Themes
Article
Three-step docking by WIPI2, ATG16L1, and ATG3 delivers LC3 to the phagophore
In a near-complete pathway from the initial membrane recruitment to the LC3 lipidation reaction, the three-step targeting of the ATG12–ATG5-ATG16L1 machinery establishes a high level of regulatory control.
Teams
Themes
Dataset
Three-step docking by WIPI2, ATG16L1, and ATG3 delivers LC3 to the phagophore: Molecular dynamics simulation data
Atomistic molecular dynamics simulation data set accompanying manuscript, “Three-step docking by WIPI2, ATG16L1 and ATG3 delivers LC3 to the phagophore.”
Teams
Themes
Lab Resource
pFastBac_Dual_GST-TEV-mCherry-TBK1
Plasmid for the expression and purification of GST-TEV-EGFP-TBK1 in Spodoptera frugiperda cells (Sf9). Internal reference: SMC1631. Used for the expression and purification of mCherry labelled TBK1 (SMC Internal No.: 1675).
Teams
Themes
Protocol
LC3 lipidation assay for ATG3 mutants
LC3 lipidation reaction assay on liposomes (SUVs, All Unilamellar vesicles).
Teams
Themes
Protocol
Generation of stable ATG3-mCherry wild-type or mutans HeLa cells with HaloTag-LC3B using lentivirus
This protocol details the generation of stable ATG3-mCherry wild-type or mutant HeLa cells with HaloTag-LC3B using lentivirus.
Teams
Themes