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Yorodumi- EMDB-11402: VAP-A engaged in in vitro membrane contact sites with the OSBP co... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11402 | |||||||||
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Title | VAP-A engaged in in vitro membrane contact sites with the OSBP construct N-PH-FFAT at 19.6 A resolution | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 19.6 Å | |||||||||
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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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11402.map.gz | 510.2 KB | EMDB map data format | |
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Header (meta data) | emd-11402-v30.xml emd-11402.xml | 11.6 KB 11.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11402_fsc.xml | 2.2 KB | Display | FSC data file |
Images | emd_11402.png | 22.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11402 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11402 | HTTPS FTP |
-Validation report
Summary document | emd_11402_validation.pdf.gz | 338.6 KB | Display | EMDB validaton report |
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Full document | emd_11402_full_validation.pdf.gz | 338.1 KB | Display | |
Data in XML | emd_11402_validation.xml.gz | 6 KB | Display | |
Data in CIF | emd_11402_validation.cif.gz | 7.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11402 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11402 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_11402.map.gz / Format: CCP4 / Size: 549.8 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 : human VAP-A
Entire | Name: human VAP-A |
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Components |
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-Supramolecule #1: human VAP-A
Supramolecule | Name: human VAP-A / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 27.9 kDa/nm |
-Macromolecule #1: Vesicle-associated membrane protein-associated protein A
Macromolecule | Name: Vesicle-associated membrane protein-associated protein A type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Sequence | String: MASASGAMAK HEQILVLDPP TDLKFKGPFT DVVTTNLKLR NPSDRKVCFK VKTTAPRRYC VRPNSGIIDP GSTVTVSVML QPFDYDPNEK SKHKFMVQTI FAPPNTSDME AVWKEAKPDE LMDSKLRCVF EMPNENDKLN DMEPSKAVPL NASKQDGPMP KPHSVSLNDT ...String: MASASGAMAK HEQILVLDPP TDLKFKGPFT DVVTTNLKLR NPSDRKVCFK VKTTAPRRYC VRPNSGIIDP GSTVTVSVML QPFDYDPNEK SKHKFMVQTI FAPPNTSDME AVWKEAKPDE LMDSKLRCVF EMPNENDKLN DMEPSKAVPL NASKQDGPMP KPHSVSLNDT ETRKLMEECK RLQGEMMKLS EENRHLRDEG LRLRKVAHSD KPGSTSTASF RDNVTSPLPS LLVVIAAIFI GFFLGKFIL |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | particle |
-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: 21 K / Instrument: LEICA 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 / 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 |