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- EMDB-15411: Single particle structure of Atg18-WT -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-15411
TitleSingle particle structure of Atg18-WT
Map datasharp map from CryoSPARC softwarew
Sample
  • Complex: Atg18
    • Protein or peptide: Autophagy-related protein 18
Keywordsautophagy / membrane remodeling / PIP binding / PI3P / PI(3 / 5)P2 / lipid binding protein / MEMBRANE PROTEIN
Function / homology
Function and homology information


regulation of phosphatidylinositol biosynthetic process / PAS complex / 1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate metabolic process / phagophore / vacuolar protein processing / positive regulation of vacuole organization / Macroautophagy / cytoplasm to vacuole targeting by the Cvt pathway / nucleophagy / pexophagy ...regulation of phosphatidylinositol biosynthetic process / PAS complex / 1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate metabolic process / phagophore / vacuolar protein processing / positive regulation of vacuole organization / Macroautophagy / cytoplasm to vacuole targeting by the Cvt pathway / nucleophagy / pexophagy / protein localization to phagophore assembly site / piecemeal microautophagy of the nucleus / phagophore assembly site membrane / late endosome to vacuole transport / phosphatidylinositol-3-phosphate binding / fungal-type vacuole membrane / phagophore assembly site / phosphatidylinositol-4-phosphate binding / phosphatidylinositol-3,5-bisphosphate binding / vacuolar membrane / extrinsic component of membrane / autophagosome assembly / ubiquitin binding / cell periphery / macroautophagy / protein transport / endosome membrane / endosome / protein-containing complex / cytosol
Similarity search - Function
: / PROPPIN / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Autophagy-related protein 18
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsMann D / Fromm S / Martinez-Sanchez A / Gopaldass N / Mayer A / Sachse C
Funding support Germany, 1 items
OrganizationGrant numberCountry
Helmholtz Association Germany
CitationJournal: To Be Published
Title: Cryo-EM structures of Atg18 oligomers reveal a tilted structural scaffold for Atg2 at the isolation membrane
Authors: Mann D / Fromm SA / Martinez-Sanchez A / Gopaldass N / Mayer A / Sachse C
History
DepositionJul 18, 2022-
Header (metadata) releaseJan 31, 2024-
Map releaseJan 31, 2024-
UpdateJan 31, 2024-
Current statusJan 31, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15411.png

Downloads & links

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Map

FileDownload / File: emd_15411.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharp map from CryoSPARC softwarew
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 256 pix.
= 214.758 Å		0.84 Å/pix.
x 256 pix.
= 214.758 Å		0.84 Å/pix.
x 256 pix.
= 214.758 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8389 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.76017296 - 1.1590412
Average (Standard dev.)-0.00026885155 (±0.019410064)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 214.7584 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15411_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_15411_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_15411_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Atg18

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

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Supramolecule #1: Atg18

SupramoleculeName: Atg18 / 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 18

MacromoleculeName: Autophagy-related protein 18 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 54.62241 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SPTINFINFN QTGTCISLGT SKGFKIFNCE PFGKFYSEDS GGYAIVEMLF STSLLALVGI GDQPALSPRR LRIINTKKHS IICEVTFPT SILSVKMNKS RLVVLLQEQI YIYDINTMRL LHTIETNPNP RGLMAMSPSV ANSYLVYPSP PKVINSEIKA H ATTNNITL ...String:
SPTINFINFN QTGTCISLGT SKGFKIFNCE PFGKFYSEDS GGYAIVEMLF STSLLALVGI GDQPALSPRR LRIINTKKHS IICEVTFPT SILSVKMNKS RLVVLLQEQI YIYDINTMRL LHTIETNPNP RGLMAMSPSV ANSYLVYPSP PKVINSEIKA H ATTNNITL SVGGNTETSF KRDQQDAGHS DISDLDQYSS FTKRDDADPT SSNGGNSSII KNGDVIVFNL ETLQPTMVIE AH KGEIAAM AISFDGTLMA TASDKGTIIR VFDIETGDKI YQFRRGTYAT RIYSISFSED SQYLAVTGSS KTVHIFKLGH SMS NNKLDS DDSNMEEAAA DDSSLDTTSI DALSDEENPT RLAREPYVDA SRKTMGRMIR YSSQKLSRRA ARTLGQIFPI KVTS LLESS RHFASLKLPV ETNSHVMTIS SIGSPIDIDT SEYPELFETG NSASTESYHE PVMKMVPIRV VSSDGYLYNF VMDPE RGGD CLILSQYSIL M

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: 7.2
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS TALOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: COUNTING / Number real images: 5117 / Average electron dose: 70.0 e/Å2

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC
Final angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 124369
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6kyb


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8afx:
Single particle structure of Atg18-WT

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