4WY4

Crystal structure of autophagic SNARE complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.136 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

ATG14 promotes membrane tethering and fusion of autophagosomes to endolysosomes.

Diao, J.Liu, R.Rong, Y.Zhao, M.Zhang, J.Lai, Y.Zhou, Q.Wilz, L.M.Li, J.Vivona, S.Pfuetzner, R.A.Brunger, A.T.Zhong, Q.

(2015) Nature 520: 563-566

  • DOI: 10.1038/nature14147

  • PubMed Abstract: 
  • Autophagy, an important catabolic pathway implicated in a broad spectrum of human diseases, begins by forming double membrane autophagosomes that engulf cytosolic cargo and ends by fusing autophagosomes with lysosomes for degradation. Membrane fusion ...

    Autophagy, an important catabolic pathway implicated in a broad spectrum of human diseases, begins by forming double membrane autophagosomes that engulf cytosolic cargo and ends by fusing autophagosomes with lysosomes for degradation. Membrane fusion activity is required for early biogenesis of autophagosomes and late degradation in lysosomes. However, the key regulatory mechanisms of autophagic membrane tethering and fusion remain largely unknown. Here we report that ATG14 (also known as beclin-1-associated autophagy-related key regulator (Barkor) or ATG14L), an essential autophagy-specific regulator of the class III phosphatidylinositol 3-kinase complex, promotes membrane tethering of protein-free liposomes, and enhances hemifusion and full fusion of proteoliposomes reconstituted with the target (t)-SNAREs (soluble N-ethylmaleimide-sensitive factor attachment protein receptors) syntaxin 17 (STX17) and SNAP29, and the vesicle (v)-SNARE VAMP8 (vesicle-associated membrane protein 8). ATG14 binds to the SNARE core domain of STX17 through its coiled-coil domain, and stabilizes the STX17-SNAP29 binary t-SNARE complex on autophagosomes. The STX17 binding, membrane tethering and fusion-enhancing activities of ATG14 require its homo-oligomerization by cysteine repeats. In ATG14 homo-oligomerization-defective cells, autophagosomes still efficiently form but their fusion with endolysosomes is blocked. Recombinant ATG14 homo-oligomerization mutants also completely lose their ability to promote membrane tethering and to enhance SNARE-mediated fusion in vitro. Taken together, our data suggest an autophagy-specific membrane fusion mechanism in which oligomeric ATG14 directly binds to STX17-SNAP29 binary t-SNARE complex on autophagosomes and primes it for VAMP8 interaction to promote autophagosome-endolysosome fusion.


    Organizational Affiliation

    1] Department of Molecular and Cellular Physiology, Stanford University, Stanford, California 94305, USA [2] Department of Structural Biology, Stanford University, Stanford, California 94305, USA [3] Department of Photon Science, Stanford University, Stanford, California 94305, USA [4] Department of Neurology and Neurological Sciences, Stanford University, Stanford, California 94305, USA [5] Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vesicle-associated membrane protein 8
A
64Homo sapiensMutation(s): 0 
Gene Names: VAMP8
Find proteins for Q9BV40 (Homo sapiens)
Go to Gene View: VAMP8
Go to UniProtKB:  Q9BV40
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Syntaxin-17
B
58Homo sapiensMutation(s): 0 
Gene Names: STX17
Find proteins for P56962 (Homo sapiens)
Go to Gene View: STX17
Go to UniProtKB:  P56962
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Synaptosomal-associated protein 29
C
78Homo sapiensMutation(s): 0 
Gene Names: SNAP29
Find proteins for O95721 (Homo sapiens)
Go to Gene View: SNAP29
Go to UniProtKB:  O95721
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Synaptosomal-associated protein 29
D
65Homo sapiensMutation(s): 0 
Gene Names: SNAP29
Find proteins for O95721 (Homo sapiens)
Go to Gene View: SNAP29
Go to UniProtKB:  O95721
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.136 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 82.850α = 90.00
b = 35.030β = 94.09
c = 104.200γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Mental HealthUnited StatesR37MH63105
Howard Hughes Medical InstituteUnited States--

Revision History 

  • Version 1.0: 2015-02-11
    Type: Initial release
  • Version 1.1: 2015-03-04
    Type: Database references
  • Version 1.2: 2015-05-06
    Type: Database references
  • Version 1.3: 2017-09-20
    Type: Advisory, Author supporting evidence, Database references, Derived calculations, Refinement description, Source and taxonomy, Structure summary