5C50

Crystal structure of the complex of human Atg101-Atg13 HORMA domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Structure of the Human Atg13-Atg101 HORMA Heterodimer: an Interaction Hub within the ULK1 Complex.

Qi, S.Kim, D.J.Stjepanovic, G.Hurley, J.H.

(2015) Structure 23: 1848-1857

  • DOI: https://doi.org/10.1016/j.str.2015.07.011
  • Primary Citation of Related Structures:  
    5C50

  • PubMed Abstract: 

    The ULK1 complex, consisting of the ULK1 protein kinase itself, FIP200, Atg13, and Atg101, controls the initiation of autophagy in animals. We determined the structure of the complex of the human Atg13 HORMA (Hop1, Rev7, Mad2) domain in complex with the full-length HORMA domain-only protein Atg101. The two HORMA domains assemble with an architecture conserved in the Mad2 conformational heterodimer and the S. pombe Atg13-Atg101 HORMA complex. The WF finger motif that is essential for function in human Atg101 is sequestered in a hydrophobic pocket, suggesting that the exposure of this motif is regulated. Benzamidine molecules from the crystallization solution mark two hydrophobic pockets that are conserved in, and unique to, animals, and are suggestive of sites that could interact with other proteins. These features suggest that the activity of the animal Atg13-Atg101 subcomplex is regulated and that it is an interaction hub for multiple partners.


  • Organizational Affiliation

    Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Autophagy-related protein 101198Homo sapiensMutation(s): 0 
Gene Names: ATG101C12orf44PP894
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BSB4 (Homo sapiens)
Explore Q9BSB4 
Go to UniProtKB:  Q9BSB4
PHAROS:  Q9BSB4
GTEx:  ENSG00000123395 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BSB4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Autophagy-related protein 13194Homo sapiensMutation(s): 0 
Gene Names: ATG13KIAA0652
UniProt & NIH Common Fund Data Resources
Find proteins for O75143 (Homo sapiens)
Explore O75143 
Go to UniProtKB:  O75143
PHAROS:  O75143
GTEx:  ENSG00000175224 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75143
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.722α = 90
b = 64.447β = 97.54
c = 94.12γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
SHELXDEphasing
PDB_EXTRACTdata extraction
Cootmodel building
ARPmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM111730

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-14
    Type: Initial release
  • Version 1.1: 2015-10-21
    Changes: Database references
  • Version 1.2: 2015-11-04
    Changes: Database references
  • Version 1.3: 2017-09-27
    Changes: Author supporting evidence, Derived calculations, Refinement description
  • Version 1.4: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.5: 2024-03-06
    Changes: Data collection, Database references