6AAF

Crystal structure of fission yeast Atg8 complexed with the helical AIM of Hfl1.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report


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Literature

Lipidation-independent vacuolar functions of Atg8 rely on its noncanonical interaction with a vacuole membrane protein

Liu, X.M.Yamasaki, A.Du, X.M.Coffman, V.C.Ohsumi, Y.Nakatogawa, H.Wu, J.Q.Noda, N.N.Du, L.L.

(2018) Elife 7

  • DOI: 10.7554/eLife.41237
  • Primary Citation of Related Structures:  
    6AAG, 6AAF

  • PubMed Abstract: 
  • The ubiquitin-like protein Atg8, in its lipidated form, plays central roles in autophagy. Yet, remarkably, Atg8 also carries out lipidation-independent functions in non-autophagic processes. How Atg8 performs its moonlighting roles is unclear. Here we report that in the fission yeast Schizosaccharomyces pombe and the budding yeast Saccharomyces cerevisiae , the lipidation-independent roles of Atg8 in maintaining normal morphology and functions of the vacuole require its interaction with a vacuole membrane protein Hfl1 (homolog of human TMEM184 proteins) ...

    The ubiquitin-like protein Atg8, in its lipidated form, plays central roles in autophagy. Yet, remarkably, Atg8 also carries out lipidation-independent functions in non-autophagic processes. How Atg8 performs its moonlighting roles is unclear. Here we report that in the fission yeast Schizosaccharomyces pombe and the budding yeast Saccharomyces cerevisiae , the lipidation-independent roles of Atg8 in maintaining normal morphology and functions of the vacuole require its interaction with a vacuole membrane protein Hfl1 (homolog of human TMEM184 proteins). Crystal structures revealed that the Atg8-Hfl1 interaction is not mediated by the typical Atg8-family-interacting motif (AIM) that forms an intermolecular β-sheet with Atg8. Instead, the Atg8-binding regions in Hfl1 proteins adopt a helical conformation, thus representing a new type of AIMs (termed helical AIMs here). These results deepen our understanding of both the functional versatility of Atg8 and the mechanistic diversity of Atg8 binding.


    Organizational Affiliation

    National Institute of Biological Sciences, Beijing, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Autophagy-related protein 8A119Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: atg8SPBP8B7.24c
UniProt
Find proteins for O94272 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore O94272 
Go to UniProtKB:  O94272
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Transmembrane protein 184 homolog C30D11.06cB31Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: SPAC30D11.06c
UniProt
Find proteins for Q09906 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore Q09906 
Go to UniProtKB:  Q09906
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.216 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.798α = 90
b = 108.866β = 90
c = 35.12γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan25111004

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-12
    Type: Initial release