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- PDB-6wqz: Structure of human ATG9A, the only transmembrane protein of the c... -

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Basic information

Entry
Database: PDB / ID: 6wqz
TitleStructure of human ATG9A, the only transmembrane protein of the core autophagy machinery
ComponentsAutophagy-related protein 9A
KeywordsMEMBRANE PROTEIN / TG9A / autophagosome / autophagy / cryoEM / molecular dynamics / transmembrane protein / membranecurvature / cellular compartments / membrane morphology / lipids
Function / homology
Function and homology information


phospholipid scramblase activity / programmed necrotic cell death / protein localization to phagophore assembly site / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / phagophore assembly site / bone morphogenesis / reticulophagy / autophagy of mitochondrion / Macroautophagy ...phospholipid scramblase activity / programmed necrotic cell death / protein localization to phagophore assembly site / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / phagophore assembly site / bone morphogenesis / reticulophagy / autophagy of mitochondrion / Macroautophagy / autophagosome assembly / autophagosome / PINK1-PRKN Mediated Mitophagy / mitochondrial membrane / trans-Golgi network / recycling endosome / recycling endosome membrane / late endosome / late endosome membrane / endosome / Golgi membrane / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / Golgi apparatus / mitochondrion / membrane
Similarity search - Function
Autophagy-related protein 9 / Autophagy protein ATG9
Similarity search - Domain/homology
Autophagy-related protein 9A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsGuardia, 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.
CitationJournal: 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.
History
DepositionApr 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
C: Autophagy-related protein 9A
F: Autophagy-related protein 9A
B: Autophagy-related protein 9A
A: Autophagy-related protein 9A
E: Autophagy-related protein 9A
D: Autophagy-related protein 9A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)492,60412
Polymers486,5736
Non-polymers6,0316
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area15930 Å2
ΔGint-155 kcal/mol
Surface area79880 Å2

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Components

#1: Protein
Autophagy-related protein 9A / APG9-like 1 / mATG9


Mass: 81095.531 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATG9A, APG9L1 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q7Z3C6
#2: Chemical
ChemComp-LMN / Lauryl Maltose Neopentyl Glycol / 2,2-didecylpropane-1,3-bis-b-D-maltopyranoside


Mass: 1005.188 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C47H88O22 / Comment: detergent*YM
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: 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 solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / C2 aperture diameter: 70 µm
Image recordingElectron dose: 57 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

Software
NameVersionClassificationNB
PHENIX1.15.2_3472:refinement
PDB_EXTRACT3.25data extraction
CTF correctionType: NONE
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 593720 / Symmetry type: POINT
RefinementCross valid method: THROUGHOUT
Displacement parametersBiso max: 93.38 Å2 / Biso mean: 33.5636 Å2 / Biso min: 7.76 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0084841
ELECTRON MICROSCOPYf_angle_d0.8256567
ELECTRON MICROSCOPYf_dihedral_angle_d9.6952822
ELECTRON MICROSCOPYf_chiral_restr0.05729
ELECTRON MICROSCOPYf_plane_restr0.006822

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