Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 147.4 kDa 
• Atom Count: 6,271 
• Modelled Residue Count: 771 
• Deposited Residue Count: 1,266 
• Unique protein chains: 2

 8DO8

Crystal structure ATG9 HDIR in complex with the ATG13:ATG101 HORMA dimer

• PDB DOI:  https://doi.org/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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 0.251 
• R-Value Work: 0.204 
• R-Value Observed: 0.205 

Literature

Structural basis for ATG9A recruitment to the ULK1 complex in mitophagy initiation.

Ren, X., Nguyen, T.N., Lam, W.K., Buffalo, C.Z., Lazarou, M., Yokom, A.L., Hurley, J.H.

(2023) Sci Adv 9: eadg2997-eadg2997

• PubMed: 36791199 
• DOI: https://doi.org/10.1126/sciadv.adg2997
• Primary Citation of Related Structures:  
  8DO8


• PubMed Abstract: 
  

The assembly of the autophagy initiation machinery nucleates autophagosome biogenesis, including in the PINK1- and Parkin-dependent mitophagy pathway implicated in Parkinson's disease. The structural interaction between the sole transmembrane autophagy protein, autophagy-related protein 9A (ATG9A), and components of the Unc-51-like autophagy activating kinase (ULK1) complex is one of the major missing links needed to complete a structural map of autophagy initiation. We determined the 2.4-Å x-ray crystallographic structure of the ternary structure of ATG9A carboxyl-terminal tail bound to the ATG13:ATG101 Hop1/Rev7/Mad2 (HORMA) dimer, which is part of the ULK1 complex. We term the interacting portion of the extreme carboxyl-terminal part of the ATG9A tail the "HORMA dimer-interacting region" (HDIR). This structure shows that the HDIR binds to the HORMA domain of ATG101 by β sheet complementation such that the ATG9A tail resides in a deep cleft at the ATG13:ATG101 interface. Disruption of this complex in cells impairs damage-induced PINK1/Parkin mitophagy mediated by the cargo receptor NDP52.

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Organizational Affiliation: 

Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94720, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Autophagy-related protein 101	A, C, E, F	218	Homo sapiens	Mutation(s): 0  Gene Names: ATG101, C12orf44, PP894
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BSB4 (Homo sapiens) Explore Q9BSB4  Go to UniProtKB:  Q9BSB4
PHAROS:  Q9BSB4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Autophagy-related protein 13	B, D	197	Homo sapiens	Mutation(s): 0  Gene Names: ATG13, KIAA0652
UniProt & NIH Common Fund Data Resources
Find proteins for O75143 (Homo sapiens) Explore O75143  Go to UniProtKB:  O75143
PHAROS:  O75143

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	AA [auth B], BA [auth C], CA [auth C], DA [auth C], EA [auth C], FA [auth C], G [auth A], GA [auth C], H [auth A], HA [auth C], I [auth A], IA [auth C], J [auth A], JA [auth C], K [auth A], KA [auth C], L [auth A], LA [auth D], M [auth A], MA [auth D], N [auth A], NA [auth D], O [auth A], OA [auth D], P [auth A], PA [auth D], Q [auth A], QA [auth D], R [auth A], RA [auth E], S [auth A], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 0.251 
• R-Value Work: 0.204 
• R-Value Observed: 0.205 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.453	α = 90
b = 139.86	β = 90
c = 147.595	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-11-23 
Deposition Author(s): Buffalo, C.Z., Ren, X., Yokom, A.L., Hurley, J.H.

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Funding Organization	Location	Grant Number
Other private	United States	ASAP-000350

Revision History  

• Version 1.0: 2022-11-23
  Type: Initial release
  
• Version 1.1: 2023-03-01
  Changes: Database references