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- PDB-8afq: Tube assembly of Atg18-PR72AA -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8afq
TitleTube assembly of Atg18-PR72AA
ComponentsAutophagy-related protein 18
KeywordsMEMBRANE PROTEIN / autophagy / membrane remodeling / PIP binding / PI3P / PI(3 / 5)P2 / lipid binding 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)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsMann, D. / Fromm, S. / Martinez-Sanchez, A. / Gopaldass, N. / Mayer, A. / Sachse, C.
Funding support Germany, 1items
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, S.A. / Martinez-Sanchez, A. / Gopaldass, N. / Mayer, A. / Sachse, C.
History
DepositionJul 18, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2023Provider: 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 18
C: Autophagy-related protein 18
D: Autophagy-related protein 18
E: Autophagy-related protein 18


Theoretical massNumber of molelcules
Total (without water)220,1834
Polymers220,1834
Non-polymers00
Water0
1
A: Autophagy-related protein 18
C: Autophagy-related protein 18
D: Autophagy-related protein 18
E: Autophagy-related protein 18
x 20


  • defined by software
  • Evidence: electron microscopy, REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE ...Evidence: electron microscopy, REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 SOFTWARE USED: UCSF CHIMERA 1.15_b42258. REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, D, E REMARK 350 BIOMT1 1 1.000000 -0.000000 -0.000000 0.00000 REMARK 350 BIOMT2 1 -0.000000 1.000000 -0.000000 0.00000 REMARK 350 BIOMT3 1 -0.000000 -0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -0.000000 1.000000 -0.000000 -0.00000 REMARK 350 BIOMT2 2 -1.000000 -0.000000 -0.000000 540.00000 REMARK 350 BIOMT3 2 -0.000000 -0.000000 1.000000 -174.60000 REMARK 350 BIOMT1 3 -0.939693 0.342020 -0.000000 431.37157 REMARK 350 BIOMT2 3 -0.342020 -0.939693 -0.000000 616.06245 REMARK 350 BIOMT3 3 -0.000000 -0.000000 1.000000 -155.20000 REMARK 350 BIOMT1 4 -0.642788 -0.766044 -0.000000 650.38465 REMARK 350 BIOMT2 4 0.766044 -0.642788 -0.000000 236.72065 REMARK 350 BIOMT3 4 -0.000000 -0.000000 1.000000 -135.80000 REMARK 350 BIOMT1 5 0.500000 -0.866025 -0.000000 368.82686 REMARK 350 BIOMT2 5 0.866025 0.500000 -0.000000 -98.82686 REMARK 350 BIOMT3 5 -0.000000 -0.000000 1.000000 -116.40000 REMARK 350 BIOMT1 6 0.984808 0.173648 -0.000000 -42.78310 REMARK 350 BIOMT2 6 -0.173648 0.984808 -0.000000 50.98691 REMARK 350 BIOMT3 6 -0.000000 -0.000000 1.000000 -97.00000 REMARK 350 BIOMT1 7 0.173648 0.984808 -0.000000 -42.78310 REMARK 350 BIOMT2 7 -0.984808 0.173648 -0.000000 489.01309 REMARK 350 BIOMT3 7 -0.000000 -0.000000 1.000000 -77.60000 REMARK 350 BIOMT1 8 -0.866025 0.500000 -0.000000 368.82686 REMARK 350 BIOMT2 8 -0.500000 -0.866025 -0.000000 638.82686 REMARK 350 BIOMT3 8 -0.000000 -0.000000 1.000000 -58.20000 REMARK 350 BIOMT1 9 -0.766044 -0.642788 -0.000000 650.38465 REMARK 350 BIOMT2 9 0.642788 -0.766044 -0.000000 303.27935 REMARK 350 BIOMT3 9 -0.000000 -0.000000 1.000000 -38.80000 REMARK 350 BIOMT1 10 0.342020 -0.939693 -0.000000 431.37157 REMARK 350 BIOMT2 10 0.939693 0.342020 -0.000000 -76.06245 REMARK 350 BIOMT3 10 -0.000000 -0.000000 1.000000 -19.40000 REMARK 350 BIOMT1 11 0.342020 0.939693 -0.000000 -76.06245 REMARK 350 BIOMT2 11 -0.939693 0.342020 -0.000000 431.37157 REMARK 350 BIOMT3 11 -0.000000 -0.000000 1.000000 19.40000 REMARK 350 BIOMT1 12 -0.766044 0.642788 -0.000000 303.27935 REMARK 350 BIOMT2 12 -0.642788 -0.766044 -0.000000 650.38465 REMARK 350 BIOMT3 12 -0.000000 -0.000000 1.000000 38.80000 REMARK 350 BIOMT1 13 -0.866025 -0.500000 -0.000000 638.82686 REMARK 350 BIOMT2 13 0.500000 -0.866025 -0.000000 368.82686 REMARK 350 BIOMT3 13 -0.000000 -0.000000 1.000000 58.20000 REMARK 350 BIOMT1 14 0.173648 -0.984808 -0.000000 489.01309 REMARK 350 BIOMT2 14 0.984808 0.173648 -0.000000 -42.78310 REMARK 350 BIOMT3 14 -0.000000 -0.000000 1.000000 77.60000 REMARK 350 BIOMT1 15 0.984808 -0.173648 -0.000000 50.98691 REMARK 350 BIOMT2 15 0.173648 0.984808 -0.000000 -42.78310 REMARK 350 BIOMT3 15 -0.000000 -0.000000 1.000000 97.00000 REMARK 350 BIOMT1 16 0.500000 0.866025 -0.000000 -98.82686 REMARK 350 BIOMT2 16 -0.866025 0.500000 -0.000000 368.82686 REMARK 350 BIOMT3 16 -0.000000 -0.000000 1.000000 116.40000 REMARK 350 BIOMT1 17 -0.642788 0.766044 -0.000000 236.72065 REMARK 350 BIOMT2 17 -0.766044 -0.642788 -0.000000 650.38465 REMARK 350 BIOMT3 17 -0.000000 -0.000000 1.000000 135.80000 REMARK 350 BIOMT1 18 -0.939693 -0.342020 -0.000000 616.06245 REMARK 350 BIOMT2 18 0.342020 -0.939693 -0.000000 431.37157 REMARK 350 BIOMT3 18 -0.000000 -0.000000 1.000000 155.20000 REMARK 350 BIOMT1 19 -0.000000 -1.000000 -0.000000 540.00000 REMARK 350 BIOMT2 19 1.000000 -0.000000 -0.000000 -0.00000 REMARK 350 BIOMT3 19 -0.000000 -0.000000 1.000000 174.60000 REMARK 350 BIOMT1 20 0.939693 -0.342020 -0.000000 108.62843 REMARK 350 BIOMT2 20 0.342020 0.939693 -0.000000 -76.06245 REMARK 350 BIOMT3 20 -0.000000 -0.000000 1.000000 194.00000
  • 4.4 MDa, 80 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)4,403,66280
Polymers4,403,66280
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation19
MethodUCSF CHIMERA

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Components

#1: 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: 55045.777 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: ATG18, AUT10, CVT18, NMR1, SVP1, YFR021W / Production host: Escherichia coli (E. coli) / References: UniProt: P43601

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Filament assembly of Atg18-PR72AA / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 99 % / Chamber temperature: 291 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 90 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 2380

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
4cryoSPARCCTF correction
7PyMOLmodel fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
11cryoSPARCclassification
12cryoSPARC3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 70 ° / Axial rise/subunit: 19.4 Å / Axial symmetry: C1
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 87223 / Symmetry type: HELICAL
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL

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