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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-8167 | |||||||||
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Title | Structure of S. cerevesiae mApe1 dodecamer | |||||||||
![]() | None | |||||||||
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![]() | dodecamer / aminopeptidase / vacuole / cvt / Hydrolase | |||||||||
Function / homology | ![]() aminopeptidase I / Cvt complex / cytoplasm to vacuole targeting by the Cvt pathway / fungal-type vacuole / metalloaminopeptidase activity / proteolysis / zinc ion binding / identical protein binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 24.0 Å | |||||||||
![]() | Sachse C / Bertipaglia C | |||||||||
![]() | ![]() Title: Higher-order assemblies of oligomeric cargo receptor complexes form the membrane scaffold of the Cvt vesicle. Authors: Chiara Bertipaglia / Sarah Schneider / Arjen J Jakobi / Abul K Tarafder / Yury S Bykov / Andrea Picco / Wanda Kukulski / Jan Kosinski / Wim Jh Hagen / Arvind C Ravichandran / Matthias ...Authors: Chiara Bertipaglia / Sarah Schneider / Arjen J Jakobi / Abul K Tarafder / Yury S Bykov / Andrea Picco / Wanda Kukulski / Jan Kosinski / Wim Jh Hagen / Arvind C Ravichandran / Matthias Wilmanns / Marko Kaksonen / John Ag Briggs / Carsten Sachse / ![]() Abstract: Selective autophagy is the mechanism by which large cargos are specifically sequestered for degradation. The structural details of cargo and receptor assembly giving rise to autophagic vesicles ...Selective autophagy is the mechanism by which large cargos are specifically sequestered for degradation. The structural details of cargo and receptor assembly giving rise to autophagic vesicles remain to be elucidated. We utilize the yeast cytoplasm-to-vacuole targeting (Cvt) pathway, a prototype of selective autophagy, together with a multi-scale analysis approach to study the molecular structure of Cvt vesicles. We report the oligomeric nature of the major Cvt cargo Ape1 with a combined 2.8 Å X-ray and negative stain EM structure, as well as the secondary cargo Ams1 with a 6.3 Å cryo-EM structure. We show that the major dodecameric cargo prApe1 exhibits a tendency to form higher-order chain structures that are broken upon interaction with the receptor Atg19 in vitro The stoichiometry of these cargo-receptor complexes is key to maintaining the size of the Cvt aggregate in vivo Using correlative light and electron microscopy, we further visualize key stages of Cvt vesicle biogenesis. Our findings suggest that Atg19 interaction limits Ape1 aggregate size while serving as a vehicle for vacuolar delivery of tetrameric Ams1. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 1.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 12 KB 12 KB | Display Display | ![]() |
Images | ![]() | 175.1 KB | ||
Filedesc metadata | ![]() | 6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5jm9MC ![]() 8166C ![]() 5jm0C ![]() 5jm6C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.9 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Mature Aminopeptidase-1 dodecamer
Entire | Name: Mature Aminopeptidase-1 dodecamer |
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Components |
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-Supramolecule #1: Mature Aminopeptidase-1 dodecamer
Supramolecule | Name: Mature Aminopeptidase-1 dodecamer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 600 KDa |
-Macromolecule #1: Vacuolar aminopeptidase 1
Macromolecule | Name: Vacuolar aminopeptidase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: aminopeptidase I |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 57.16243 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MEEQREILEQ LKKTLQMLTV EPSKNNQIAN EEKEKKENEN SWCILEHNYE DIAQEFIDFI YKNPTTYHVV SFFAELLDKH NFKYLSEKS NWQDSIGEDG GKFYTIRNGT NLSAFILGKN WRAEKGVGVI GSHVDALTVK LKPVSFKDTA EGYGRIAVAP Y GGTLNELW ...String: MEEQREILEQ LKKTLQMLTV EPSKNNQIAN EEKEKKENEN SWCILEHNYE DIAQEFIDFI YKNPTTYHVV SFFAELLDKH NFKYLSEKS NWQDSIGEDG GKFYTIRNGT NLSAFILGKN WRAEKGVGVI GSHVDALTVK LKPVSFKDTA EGYGRIAVAP Y GGTLNELW LDRDLGIGGR LLYKKKGTNE IKSALVDSTP LPVCRIPSLA PHFGKPAEGP FDKEDQTIPV IGFPTPDEEG NE PPTDDEK KSPLFGKHCI HLLRYVAKLA GVEVSELIQM DLDLFDVQKG TIGGIGKHFL FAPRLDDRLC SFAAMIALIC YAK DVNTEE SDLFSTVTLY DNEEIGSLTR QGAKGGLLES VVERSSSAFT KKPVDLHTVW ANSIILSADV NHLYNPNFPE VYLK NHFPV PNVGITLSLD PNGHMATDVV GTALVEELAR RNGDKVQYFQ IKNNSRSGGT IGPSLASQTG ARTIDLGIAQ LSMHS IRAA TGSKDVGLGV KFFNGFFKHW RSVYDEFGEL UniProtKB: Vacuolar aminopeptidase 1 |
-Experimental details
-Structure determination
Method | negative staining |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 Component:
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Staining | Type: NEGATIVE / Material: Uranyl acetate | |||||||||
Details | The sample was purified using a GraFix gradient. |
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Electron microscopy
Microscope | FEI/PHILIPS CM12 |
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Image recording | Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 53000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC |