4YK8

Crystal structure of the Atg101-Atg13 complex from fission yeast


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.267 
  • R-Value Observed: 0.267 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure of the Atg101-Atg13 complex reveals essential roles of Atg101 in autophagy initiation.

Suzuki, H.Kaizuka, T.Mizushima, N.Noda, N.N.

(2015) Nat Struct Mol Biol 22: 572-580

  • DOI: https://doi.org/10.1038/nsmb.3036
  • Primary Citation of Related Structures:  
    4YK8

  • PubMed Abstract: 

    Atg101 is an essential component of the autophagy-initiating ULK complex in higher eukaryotes, but it is absent from the functionally equivalent Atg1 complex in budding yeast. Here, we report the crystal structure of the fission yeast Atg101-Atg13 complex. Atg101 has a Hop1, Rev7 and Mad2 (HORMA) architecture similar to that of Atg13. Mad2 HORMA has two distinct conformations (O-Mad2 and C-Mad2), and, intriguingly, Atg101 resembles O-Mad2 rather than the C-Mad2-like Atg13. Atg13 HORMA from higher eukaryotes possesses an inherently unstable fold, which is stabilized by Atg101 via interactions analogous to those between O-Mad2 and C-Mad2. Mutational studies revealed that Atg101 is responsible for recruiting downstream factors to the autophagosome-formation site in mammals via a newly identified WF finger. These data define the molecular functions of Atg101, providing a basis for elucidating the molecular mechanisms of mammalian autophagy initiation by the ULK complex.


  • Organizational Affiliation

    Institute of Microbial Chemistry (BIKAKEN), Tokyo, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Meiotically up-regulated gene 66 protein187Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: mug66atg101SPAC25H1.03
UniProt
Find proteins for O13978 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore O13978 
Go to UniProtKB:  O13978
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO13978
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Autophagy protein 13242Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: atg13mug78SPAC4F10.07c
UniProt
Find proteins for O36019 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore O36019 
Go to UniProtKB:  O36019
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO36019
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.267 
  • R-Value Observed: 0.267 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.822α = 90
b = 83.389β = 106.22
c = 91.113γ = 90
Software Package:
Software NamePurpose
CNSrefinement
REFMACrefinement
Cootmodel building
PHASESphasing
HKL-2000data processing
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Science and Technology AgencyJapanCREST
Ministry of Education, Culture, Sports, Science and Technology of JapanJapan25111004

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-03
    Type: Initial release
  • Version 1.1: 2015-06-10
    Changes: Database references
  • Version 1.2: 2015-07-22
    Changes: Database references
  • Version 1.3: 2020-02-05
    Changes: Data collection, Derived calculations, Source and taxonomy
  • Version 1.4: 2024-03-20
    Changes: Data collection, Database references