5XV6

Crystal structure of ATG101-ATG13HORMA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.455 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The C-terminal region of ATG101 bridges ULK1 and PtdIns3K complex in autophagy initiation.

Kim, B.-W.Jin, Y.Kim, J.Kim, J.H.Jung, J.Kang, S.Kim, I.Y.Kim, J.Cheong, H.Song, H.K.

(2018) Autophagy 14: 2104-2116

  • DOI: 10.1080/15548627.2018.1504716
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The initiation of macroautophagy/autophagy is tightly regulated by the upstream ULK1 kinase complex, which affects many downstream factors including the PtdIns3K complex. The phosphorylation of the right position at the right time on downstream molec ...

    The initiation of macroautophagy/autophagy is tightly regulated by the upstream ULK1 kinase complex, which affects many downstream factors including the PtdIns3K complex. The phosphorylation of the right position at the right time on downstream molecules is governed by proper complex formation. One component of the ULK1 complex, ATG101, known as an accessory protein, is a stabilizer of ATG13 in cells. The WF finger region of ATG101 plays an important role in the recruitment of WIPI1 (WD repeat domain, phosphoinositide interacting protein 1) and ZFYVE1 (zinc finger FYVE-type containing 1). Here, we report that the C-terminal region identified in the structure of the human ATG101-ATG13 HORMA complex is responsible for the binding of the PtdIns3K complex. This region adopts a β-strand conformation in free ATG101, but either an α-helix or random coil in our ATG101-ATG13 HORMA complex, which protrudes from the core and interacts with other molecules. The C-terminal deletion of ATG101 shows a significant defect in the interaction with PtdIns3K components and subsequently impairs autophagosome formation. This result clearly presents an additional role of ATG101 for bridging the ULK1 and PtdIns3K complexes in the mammalian autophagy process. Abbreviations: ATG: autophagy related; BECN1: beclin 1; GFP: green fluorescent protein; HORMA: Hop1p/Rev7p/MAD2; HsATG13 HORMA : HORMA domain of ATG13 from Homo sapiens; KO: knockout; MAD2: mitotic arrest deficient 2 like 1; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; PIK3C3/VPS34: phosphatidylinositol 3-kinase catalytic subunit type 3; PIK3R4/VPS15: phosphoinositide-3-kinase regulatory subunit 4; PtdIns3K: phosphatidylinositol 3-kinase; RB1CC1/FIP200: RB1 inducible coiled-coil 1; SAXS: small-angle X-ray scattering; ScAtg13 HORMA : HORMA domain of Atg13 from Sccharomyces cerevisiae; SEC-SAXS: size-exclusion chromatography with small-angle X-ray scattering; SpAtg13 HORMA : HORMA domain of Atg13 from Schizosaccharomyces pombe; SQSTM1/p62: sequestosome 1; ULK1: unc51-like autophagy activating kinase 1; UVRAG: UV radiation resistance associated; WIPI1: WD repeat domain: phosphoinositide interacting 1; ZFYVE1/DFCP1: zinc finger FYVE-type containing 1.


    Organizational Affiliation

    a Department of Life Sciences , Korea University , Seongbuk-gu, Seoul , Republic of Korea.,d Department of Life and Nanopharmaceutical Sciences , Graduate School , Seongbuk-gu, Seoul , Republic of Korea.,e Department of Oral Biochemistry and Molecular BiologySchool of Dentistry , Kyung Hee University , Seoul , Republic of Korea.,c Tumor Microenvironment Branch , Research Institute, National Cancer Center , Goyang , Republic of Korea.,b Department of Cancer Biomedical Science , National Cancer Center Graduate School of Cancer Science and Policy , Seongbuk-gu, Seoul , Republic of Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Autophagy-related protein 13
A
190Homo sapiensMutation(s): 0 
Gene Names: ATG13 (KIAA0652)
Find proteins for O75143 (Homo sapiens)
Go to Gene View: ATG13
Go to UniProtKB:  O75143
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Autophagy-related protein 101
B
218Homo sapiensMutation(s): 3 
Gene Names: ATG101 (C12orf44)
Find proteins for Q9BSB4 (Homo sapiens)
Go to Gene View: ATG101
Go to UniProtKB:  Q9BSB4
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.455 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.225 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 84.019α = 90.00
b = 123.485β = 90.00
c = 99.798γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-06-26 
  • Released Date: 2018-07-04 
  • Deposition Author(s): Kim, B.-W., Song, H.K.

Revision History 

  • Version 1.0: 2018-07-04
    Type: Initial release
  • Version 1.1: 2019-01-16
    Type: Data collection, Database references