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- EMDB-55395: Atg2-Atg18 complex from yeast -

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Basic information

Entry
Database: EMDB / ID: EMD-55395
TitleAtg2-Atg18 complex from yeast
Map dataAtg2-Atg18 complex from yeast
Sample
  • Complex: Atg2-Atg18 complex
    • Protein or peptide: Autophagy-related protein 2
    • Protein or peptide: Autophagy-related protein 18
Keywordsautophagy / lipid transfer / Atg2 / Atg18 / complex / LIPID TRANSPORT
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)
Methodsingle 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, 6 items
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, 2025-
Header (metadata) releaseJun 3, 2026-
Map releaseJun 3, 2026-
UpdateJun 3, 2026-
Current statusJun 3, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55395.png

Downloads & links

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Map

FileDownload / File: emd_55395.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAtg2-Atg18 complex from yeast
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 512 pix.
= 473.088 Å		0.92 Å/pix.
x 512 pix.
= 473.088 Å		0.92 Å/pix.
x 512 pix.
= 473.088 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.924 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-0.75914025 - 0.9920367
Average (Standard dev.)-0.00011521643 (±0.010524545)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 473.088 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Atg2-Atg18 complex from yeast, half-map B

Fileemd_55395_half_map_1.map
AnnotationAtg2-Atg18 complex from yeast, half-map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Atg2-Atg18 complex from yeast, half-map A

Fileemd_55395_half_map_2.map
AnnotationAtg2-Atg18 complex from yeast, half-map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Atg2-Atg18 complex

EntireName: Atg2-Atg18 complex
Components
  • Complex: Atg2-Atg18 complex
    • Protein or peptide: Autophagy-related protein 2
    • Protein or peptide: Autophagy-related protein 18

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Supramolecule #1: Atg2-Atg18 complex

SupramoleculeName: Atg2-Atg18 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Autophagy-related protein 2

MacromoleculeName: Autophagy-related protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 178.615578 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MAFWLPQNIQ KRLLLYVLQQ ISLFSNIDLS NLDVSIGSKS HFSFHDVNLS LDDLNIPNVQ INEGIVDELV LKLTVSGGVE IDGSGLRFI MTPLYSSGSQ ELHSDFLVKS IQDLTNSMLQ FSDPLTTYNR YKEDDISSSD SSSDLNSNIE ASKPAANGSY T LQNMRNKA ...String:
MAFWLPQNIQ KRLLLYVLQQ ISLFSNIDLS NLDVSIGSKS HFSFHDVNLS LDDLNIPNVQ INEGIVDELV LKLTVSGGVE IDGSGLRFI MTPLYSSGSQ ELHSDFLVKS IQDLTNSMLQ FSDPLTTYNR YKEDDISSSD SSSDLNSNIE ASKPAANGSY T LQNMRNKA LNVALAKLKI ALKDVTIRFI VNDRDPSDNI VEVHLESIQL ITTDANLRHI NIENITISSI QKQAVPDSPV HP FNNDDLS QSVYLSKMEA TSLYMSAMEE QSNEDPSEPQ VTQEEQENDK CKESLMEINN LNIAFKGLSS VNDLRMSNIV IDI QDVHLA IHKIVEIKNS TLKNIIDIIV THLDANESFS CQDSQSPSPD KQEPSALSSV DIKCIYLNLG QDITVILKSF KLEQ KENNS LAFSLGSFYS NSSPLTISHK TKPLLTGEQT PQSIALNMGD ELDIIISHDG IAHFFKIFQF VSKCMSFYQN KSKGM MPQI ASDTKRTVQL TSKAVKLSLK FPYFLLCFQV SPFIYDSNRE LYIELVDVFK KLPSRCTKIL TMSSITISNL QSPLQL GSY DDTLKEALIY SSVHAIIKEV IFNEEYSGIV QLVEDISAFG KLFTDSKNSE CTGKSKSKRG SFLQRSVRVL NSSRFVY KQ SLSANFSLKI DSMKLKVSEI IGPQFGSVEA LLSNNFFAIT DDSQIVYFTK NLKVERKTPS LLEPQEIMSV VLNKAVNE P VLYVHRRANG KLKVIFNNIR IHYYARWLEI LKKNIGPDNA SSKDEPVSQK LSKKQPTSGF PWELKCLDCS LILHPFRLK SVMVIVLDNL TTGGSSFIPQ AKLLSKANTL FLIDDYQNFK IQKDKNWPSL INFYAGQGFS AIGKIDTLNF LINKSDGALL LDCKIEQVG LSLCADSFQT FCQLCIDLKY PQTFPDEEKF RTQLKNPIDV FKDIDCDLFN SAFIRENNHQ NDYDSVHLVD S FLDKTHEF NNGARSKLSS QGSYEMDSSS GTATGGILLP HESYLDSAQP KEEDTPPIAS KEQERDVDIR GSIDVEKVVI KL FDGYDWK YTRKFIANTV EKLDKELSKA EASSSKSNVP QSEANIFDSI YISANKNNVT DLRRNLDGEI QGVQNSFSDV SKV NLRPSK HYKALIQLNK VHVNLKNYRV DEPDESNSDN STDVLNRCVV SIYEFEIIDN VPTSTWNKFV TLLKHEPWPH SSPM FLLDL EFIRPIDFLQ AVELVMQLNV APLRLHVDQD TLEFLIRFLG FKDKRFELID EYPDIVFIQK FSTNSIKLRL DYKPK KVDY AGLRSGQTSE LMNFFTLDGS KIILKSVVLY GLNGFDELNN KLKAIWTPDI TKKQLPGVLE GLAPVRSFMA IGSGVK TLV TVLMSEYRQE GHLGRSLKKG GNVFLKTTTG DFVKLGVKLT SGTQAILENT EELFGGVGSN GRVYDASKFG SADGADS DT AAVLDLDTLF EEDQLVGSKY SRIRDHEPTA VVIDMSSPGD HNEPTIVSLY ADQPLDLPTG LKEAYSSLEK HMHIAYDA V WRAKGQMKDD KRGGPSAAAV YVARAAPVAI IRPLIGATEA VSKTLQGIAN QVDKTHNEQI NDKYKSNRTD S

UniProtKB: Autophagy-related protein 2

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Macromolecule #2: Autophagy-related protein 18

MacromoleculeName: Autophagy-related protein 18 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 60.148598 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSDSSPTINF INFNQTGTCI SLGTSKGFKI FNCEPFGKFY SEDSGGYAIV EMLFSTSLLA LVGIGDQPAL SPRRLRIINT KKHSIICEV TFPTSILSVK MNKSRLVVLL QEQIYIYDIN TMRLLHTIET NPNPRGLMAM SPSVANSYLV YPSPPKVINS E IKAHATTN ...String:
MSDSSPTINF INFNQTGTCI SLGTSKGFKI FNCEPFGKFY SEDSGGYAIV EMLFSTSLLA LVGIGDQPAL SPRRLRIINT KKHSIICEV TFPTSILSVK MNKSRLVVLL QEQIYIYDIN TMRLLHTIET NPNPRGLMAM SPSVANSYLV YPSPPKVINS E IKAHATTN NITLSVGGNT ETSFKRDQQD AGHSDISDLD QYSSFTKRDD ADPTSSNGGN SSIIKNGDVI VFNLETLQPT MV IEAHKGE IAAMAISFDG TLMATASDKG TIIRVFDIET GDKIYQFRRG TYATRIYSIS FSEDSQYLAV TGSSKTVHIF KLG HSMSNN KLDSDDSNME EAAADDSSLD TTSIDALSDE ENPTRLAREP YVDASRKTMG RMIRYSSQKL SRRAARTLGQ IFPI KVTSL LESSRHFASL KLPVETNSHV MTISSIGSPI DIDTSEYPEL FETGNSASTE SYHEPVMKMV PIRVVSSDGY LYNFV MDPE RGGDCLILSQ YSILMDRTLQ VDKRRWKKNF IAVSAANRFK KISSSGALDY DIPTTASVDG S

UniProtKB: Autophagy-related protein 18

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 97431
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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