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Yorodumi- EMDB-0413: Vesicle-plasma interface under the docked vesicles in NGF-differe... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0413 | |||||||||
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Title | Vesicle-plasma interface under the docked vesicles in NGF-differentiated PC12 cells without imposed symmetry | |||||||||
Map data | Vesicle-plasma interface under the docked vesicles in NGF-differentiated PC12 cells without imposed symmetry | |||||||||
Sample |
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Biological species | Rattus norvegicus (Norway rat) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 50.0 Å | |||||||||
Authors | Li X / Radhakrishnan A / Grushin K / Krishnakumar S / Liu J / Rothman J | |||||||||
Citation | Journal: FEBS Lett / Year: 2019 Title: Symmetrical organization of proteins under docked synaptic vesicles. Authors: Xia Li / Abhijith Radhakrishnan / Kirill Grushin / Ravikiran Kasula / Arunima Chaudhuri / Sujatha Gomathinayagam / Shyam S Krishnakumar / Jun Liu / James E Rothman / Abstract: During calcium-regulated exocytosis, the constitutive fusion machinery is 'clamped' in a partially assembled state until synchronously released by calcium. The protein machinery involved in this ...During calcium-regulated exocytosis, the constitutive fusion machinery is 'clamped' in a partially assembled state until synchronously released by calcium. The protein machinery involved in this process is known, but the supra-molecular architecture and underlying mechanisms are unclear. Here, we use cryo-electron tomography analysis in nerve growth factor-differentiated neuro-endocrine (PC12) cells to delineate the organization of the release machinery under the docked vesicles. We find that exactly six exocytosis modules, each likely consisting of a single SNAREpin with its bound Synaptotagmins, Complexin, and Munc18 proteins, are symmetrically arranged at the vesicle-PM interface. Mutational analysis suggests that the symmetrical organization is templated by circular oligomers of Synaptotagmin. The observed arrangement, including its precise radial positioning, is in-line with the recently proposed 'buttressed ring hypothesis'. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0413.map.gz | 6.1 MB | EMDB map data format | |
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Header (meta data) | emd-0413-v30.xml emd-0413.xml | 8.5 KB 8.5 KB | Display Display | EMDB header |
Images | emd_0413.png | 186.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0413 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0413 | HTTPS FTP |
-Validation report
Summary document | emd_0413_validation.pdf.gz | 78.7 KB | Display | EMDB validaton report |
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Full document | emd_0413_full_validation.pdf.gz | 77.8 KB | Display | |
Data in XML | emd_0413_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0413 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0413 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_0413.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Vesicle-plasma interface under the docked vesicles in NGF-differentiated PC12 cells without imposed symmetry | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 5.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Docked synaptic vesicle
Entire | Name: Docked synaptic vesicle |
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Components |
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-Supramolecule #1: Docked synaptic vesicle
Supramolecule | Name: Docked synaptic vesicle / type: organelle_or_cellular_component / ID: 1 / Parent: 0 Details: Synaptic vesicles in neurites developed from nerve growth factor (NGF)-differentiated pheochromocytoma (PC12) cells |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) / Cell: PC12 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil R2/1 / Material: GOLD |
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.47 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 50.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number subtomograms used: 2434 |
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Extraction | Number tomograms: 574 / Number images used: 4758 |
Final angle assignment | Type: OTHER |