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- PDB-9t0c: Atg2-Atg18 complex from yeast -

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Basic information

Entry
Database: PDB / ID: 9t0c
TitleAtg2-Atg18 complex from yeast
Components
  • Autophagy-related protein 18
  • Autophagy-related protein 2
KeywordsLIPID TRANSPORT / autophagy / lipid transfer / Atg2 / Atg18 / complex
Function / homology
Function and homology information


extrinsic component of phagophore assembly site membrane / phagophore / lipid transfer activity / glycophagy / cytoplasm to vacuole targeting by the Cvt pathway / nucleophagy / phagophore assembly site membrane / autophagy of mitochondrion / piecemeal microautophagy of the nucleus / phosphatidylinositol-3-phosphate binding ...extrinsic component of phagophore assembly site membrane / phagophore / lipid transfer activity / glycophagy / cytoplasm to vacuole targeting by the Cvt pathway / nucleophagy / phagophore assembly site membrane / autophagy of mitochondrion / piecemeal microautophagy of the nucleus / phosphatidylinositol-3-phosphate binding / pexophagy / phagophore assembly site / reticulophagy / vacuolar membrane / autophagosome assembly / protein-membrane adaptor activity / macroautophagy / autophagy / protein transport / endosome membrane / endoplasmic reticulum membrane / protein-containing complex / cytoplasm / cytosol
Similarity search - Function
Autophagy-related protein 2 / Autophagy-related protein 2 / : / PROPPIN / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Autophagy-related protein 18 / Autophagy-related protein 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsChumpen Ramirez, S. / Shvarev, D. / Vargas Duarte, P. / Milach, J. / Lang, E. / Kuchenbuch, S. / Reggiori, F. / Moeller, A. / Ungermann, C.
Funding support Germany, Denmark, 6items
OrganizationGrant numberCountry
German Research Foundation (DFG)448135520 Germany
German Research Foundation (DFG)516911046 Germany
German Research Foundation (DFG)37802001 Germany
German Research Foundation (DFG)516908673 Germany
German Research Foundation (DFG)455249646 Germany
Novo Nordisk Foundation0066384 Denmark
CitationJournal: EMBO J / Year: 2026
Title: Atg18 interaction positions Atg2 for efficient lipid transfer into phagophore elongation.
Authors: Sabrina Chumpen Ramirez / Dmitry Shvarev / Prado Vargas Duarte / Yara Ahmed / Jana Milach / Emma Lang / Stefan Kuchenbuch / Stefano Vanni / Fulvio Reggiori / Arne Moeller / Christian Ungermann /
Abstract: During macroautophagy, the de novo formation of the autophagosome at a membrane contact site (MCS) with the endoplasmic reticulum requires directional lipid flux for the growth of the initial ...During macroautophagy, the de novo formation of the autophagosome at a membrane contact site (MCS) with the endoplasmic reticulum requires directional lipid flux for the growth of the initial phagophore before its sealing into an autophagosome and subsequent fusion with the lysosome/vacuole. It remains unclear, however, how the formation of this specialized MCS and the directionality of the lipid flux are controlled. Here, we present the structure of the key lipid transfer protein Atg2 from yeast solved together with its Atg18 binding partner, a phosphatidylinositol-3-phosphate (PtdIns3P) effector, using cryo-electron microscopy. We reveal a new interface in Atg2 that, together with PtdIns3P, is required for Atg18 recruitment and lipid transfer activity. Furthermore, we visualize lipid densities along the internal hydrophobic cavity of Atg2, providing structural evidence that Atg2 cavity is filled with lipids throughout the entire length, even when Atg2 is cytosolic. Finally, molecular dynamics simulations show that the complex generates membrane curvature, efficiently positioning the lipid channel of Atg2 towards the membrane to promote lipid transfer into the elongating phagophore.
History
DepositionOct 16, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Autophagy-related protein 2
B: Autophagy-related protein 18


Theoretical massNumber of molelcules
Total (without water)238,7642
Polymers238,7642
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Autophagy-related protein 2 / Sporulation-specific protein 72


Mass: 178615.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ATG2, APG2, AUT8, SPO72, YNL242W, N1106 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P53855
#2: Protein Autophagy-related protein 18 / Cytoplasm to vacuole targeting protein 18 / Needed for premeiotic replication protein 1 / Swollen ...Cytoplasm to vacuole targeting protein 18 / Needed for premeiotic replication protein 1 / Swollen vacuole phenotype protein 1


Mass: 60148.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ATG18, AUT10, CVT18, NMR1, SVP1, SCY_1768 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A7A258
Has protein modificationN

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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: Atg2-Atg18 complex / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 97431 / Symmetry type: POINT
RefinementHighest resolution: 4.5 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0026120
ELECTRON MICROSCOPYf_angle_d0.5388276
ELECTRON MICROSCOPYf_dihedral_angle_d4.609839
ELECTRON MICROSCOPYf_chiral_restr0.047989
ELECTRON MICROSCOPYf_plane_restr0.0031050

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