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Yorodumi- EMDB-11427: Representative tomogram of in vitro membrane contact sites betwee... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11427 | |||||||||
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Title | Representative tomogram of in vitro membrane contact sites between VAP-A and N-PH-FFAT | |||||||||
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Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | electron tomography / cryo EM | |||||||||
Authors | de la Mora E / diCicco A / Dezi M / Levy D | |||||||||
Citation | Journal: Nat Commun / Year: 2021 Title: Nanoscale architecture of a VAP-A-OSBP tethering complex at membrane contact sites. Authors: Eugenio de la Mora / Manuela Dezi / Aurélie Di Cicco / Joëlle Bigay / Romain Gautier / John Manzi / Joël Polidori / Daniel Castaño-Díez / Bruno Mesmin / Bruno Antonny / Daniel Lévy / Abstract: Membrane contact sites (MCS) are subcellular regions where two organelles appose their membranes to exchange small molecules, including lipids. Structural information on how proteins form MCS is ...Membrane contact sites (MCS) are subcellular regions where two organelles appose their membranes to exchange small molecules, including lipids. Structural information on how proteins form MCS is scarce. We designed an in vitro MCS with two membranes and a pair of tethering proteins suitable for cryo-tomography analysis. It includes VAP-A, an ER transmembrane protein interacting with a myriad of cytosolic proteins, and oxysterol-binding protein (OSBP), a lipid transfer protein that transports cholesterol from the ER to the trans Golgi network. We show that VAP-A is a highly flexible protein, allowing formation of MCS of variable intermembrane distance. The tethering part of OSBP contains a central, dimeric, and helical T-shape region. We propose that the molecular flexibility of VAP-A enables the recruitment of partners of different sizes within MCS of adjustable thickness, whereas the T geometry of the OSBP dimer facilitates the movement of the two lipid-transfer domains between membranes. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11427.map.gz | 1.1 GB | EMDB map data format | |
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Header (meta data) | emd-11427-v30.xml emd-11427.xml | 10.6 KB 10.6 KB | Display Display | EMDB header |
Images | emd_11427.png | 130.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11427 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11427 | HTTPS FTP |
-Validation report
Summary document | emd_11427_validation.pdf.gz | 271.8 KB | Display | EMDB validaton report |
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Full document | emd_11427_full_validation.pdf.gz | 271.4 KB | Display | |
Data in XML | emd_11427_validation.xml.gz | 4.7 KB | Display | |
Data in CIF | emd_11427_validation.cif.gz | 5.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11427 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11427 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_11427.map.gz / Format: CCP4 / Size: 1.2 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 6.8 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 : In vitro system formation of membrane contact sites between human...
Entire | Name: In vitro system formation of membrane contact sites between human VAP-A and the OSBP construct N-PH-FFAT |
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Components |
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-Supramolecule #1: In vitro system formation of membrane contact sites between human...
Supramolecule | Name: In vitro system formation of membrane contact sites between human VAP-A and the OSBP construct N-PH-FFAT type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | 3D array |
-Sample preparation
Buffer | pH: 7.4 Component:
Details: 50 mM HEPES pH 7.4 120 mM potassium acetate | |||||||||
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Grid | Model: Homemade / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 98 % / Chamber temperature: 294 K / Instrument: LEICA PLUNGER | |||||||||
Sectioning | Other: NO SECTIONING | |||||||||
Fiducial marker | Manufacturer: Home-made / Diameter: 6 nm |
-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 / Number grids imaged: 2 / Average electron dose: 3.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Algorithm: BACK PROJECTION / Software - Name: eTomo / Number images used: 41 |
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CTF correction | Software - Name: CTFPHASEFLIP |