|Entry||Database: PDB / ID: 6wr4|
|Title||Structure of human ATG9A, the only transmembrane protein of the core autophagy machinery|
|Components||Autophagy-related protein 9A|
|Keywords||MEMBRANE PROTEIN / TG9A / autophagosome / autophagy / cryoEM / molecular dynamics / transmembrane protein / membranecurvature / cellular compartments / membrane morphology / lipids|
|Function / homology|
Function and homology information
late nucleophagy / protein localization to phagophore assembly site / phagophore assembly site / autophagy of mitochondrion / autophagosome assembly / autophagosome / late endosome membrane / recycling endosome / trans-Golgi network / protein transport ...late nucleophagy / protein localization to phagophore assembly site / phagophore assembly site / autophagy of mitochondrion / autophagosome assembly / autophagosome / late endosome membrane / recycling endosome / trans-Golgi network / protein transport / late endosome / endosome / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / membrane / integral component of membrane
Autophagy-related protein 9
Autophagy-related protein 9A
|Biological species||Homo sapiens (human)|
|Method||ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å|
|Authors||Guardia, C.M. / Tan, X. / Lian, T. / Rana, M.S. / Zhou, W. / Christenson, E.T. / Lowry, A.J. / Faraldo-Gomez, J.D. / Bonifacino, J.S. / Jiang, J. / Banerjee, A.|
|Citation||Journal: Cell Rep / Year: 2020|
Title: Structure of Human ATG9A, the Only Transmembrane Protein of the Core Autophagy Machinery.
Authors: Carlos M Guardia / Xiao-Feng Tan / Tengfei Lian / Mitra S Rana / Wenchang Zhou / Eric T Christenson / Augustus J Lowry / José D Faraldo-Gómez / Juan S Bonifacino / Jiansen Jiang / Anirban Banerjee /
Abstract: Autophagy is a catabolic process involving capture of cytoplasmic materials into double-membraned autophagosomes that subsequently fuse with lysosomes for degradation of the materials by lysosomal ...Autophagy is a catabolic process involving capture of cytoplasmic materials into double-membraned autophagosomes that subsequently fuse with lysosomes for degradation of the materials by lysosomal hydrolases. One of the least understood components of the autophagy machinery is the transmembrane protein ATG9. Here, we report a cryoelectron microscopy structure of the human ATG9A isoform at 2.9-Å resolution. The structure reveals a fold with a homotrimeric domain-swapped architecture, multiple membrane spans, and a network of branched cavities, consistent with ATG9A being a membrane transporter. Mutational analyses support a role for the cavities in the function of ATG9A. In addition, structure-guided molecular simulations predict that ATG9A causes membrane bending, explaining the localization of this protein to small vesicles and highly curved edges of growing autophagosomes.
SummaryFull reportAbout validation report
|Structure viewer||Molecule: |
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A: Autophagy-related protein 9A
B: Autophagy-related protein 9A
C: Autophagy-related protein 9A
Mass: 94551.031 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATG9A, APG9L1 / Production host: Homo sapiens (human) / References: UniProt: Q7Z3C6
Mass: 1005.188 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C47H88O22 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
|Has ligand of interest||Y|
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction|
|Component||Name: Autophagy Related 9A with LMNG / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT|
|Source (natural)||Organism: Homo sapiens (human)|
|Source (recombinant)||Organism: Homo sapiens (human)|
|Buffer solution||pH: 8|
|Specimen||Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Specimen support||Details: unspecified|
|Vitrification||Cryogen name: ETHANE|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Microscopy||Model: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELDBright-field microscopy / C2 aperture diameter: 70 µm|
|Image recording||Electron dose: 57 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)|
|CTF correction||Type: NONE|
|3D reconstruction||Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 646291 / Symmetry type: POINT|
|Refinement||Cross valid method: THROUGHOUT|
|Displacement parameters||Biso max: 0 Å2 / Biso mean: 0 Å2 / Biso min: 0 Å2|
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