Experimental Data Snapshot

  • Resolution: 1.41 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


The cholesterol transfer protein GRAMD1A regulates autophagosome biogenesis.

Laraia, L.Friese, A.Corkery, D.P.Konstantinidis, G.Erwin, N.Hofer, W.Karatas, H.Klewer, L.Brockmeyer, A.Metz, M.Scholermann, B.Dwivedi, M.Li, L.Rios-Munoz, P.Kohn, M.Winter, R.Vetter, I.R.Ziegler, S.Janning, P.Wu, Y.W.Waldmann, H.

(2019) Nat Chem Biol 15: 710-720

  • DOI: https://doi.org/10.1038/s41589-019-0307-5
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Autophagy mediates the degradation of damaged proteins, organelles and pathogens, and plays a key role in health and disease. Thus, the identification of new mechanisms involved in the regulation of autophagy is of major interest. In particular, little is known about the role of lipids and lipid-binding proteins in the early steps of autophagosome biogenesis. Using target-agnostic, high-content, image-based identification of indicative phenotypic changes induced by small molecules, we have identified autogramins as a new class of autophagy inhibitor. Autogramins selectively target the recently discovered cholesterol transfer protein GRAM domain-containing protein 1A (GRAMD1A, which had not previously been implicated in autophagy), and directly compete with cholesterol binding to the GRAMD1A StART domain. GRAMD1A accumulates at sites of autophagosome initiation, affects cholesterol distribution in response to starvation and is required for autophagosome biogenesis. These findings identify a new biological function of GRAMD1A and a new role for cholesterol in autophagy.

  • Organizational Affiliation

    Chemical Genomics Centre of the Max Planck Society, Dortmund, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GRAM domain-containing protein 1C192Homo sapiensMutation(s): 0 
Gene Names: GRAMD1CUNQ2543/PRO6095
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IYS0 (Homo sapiens)
Explore Q8IYS0 
Go to UniProtKB:  Q8IYS0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IYS0
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.41 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.32α = 90
b = 73.85β = 99.31
c = 45.34γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
PDB_EXTRACTdata extraction
XSCALEdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-19
    Type: Initial release
  • Version 1.1: 2019-07-03
    Changes: Data collection, Database references
  • Version 1.2: 2019-07-10
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-25
    Changes: Data collection