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- EMDB-11455: Representative tomogram of in vitro membrane contact sites betwee... -

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Basic information

Entry
Database: EMDB / ID: EMD-11455
TitleRepresentative tomogram of in vitro membrane contact sites between VAP-A and OSBP.
Map data
Sample
  • Complex: VAP-A and OSBP
Biological speciesHomo sapiens (human)
Methodelectron tomography / cryo EM
Authorsde la Mora E / Dezi M / diCicco A / Bigay J / Gautier R / Manzi J / Polidori J / Castano-Diez D / Mesmin B / Antonny B / Levy D
CitationJournal: 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
DepositionJul 24, 2020-
Header (metadata) releaseMay 12, 2021-
Map releaseMay 12, 2021-
UpdateNov 24, 2021-
Current statusNov 24, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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Supplemental images

emd_11455.png

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Map

FileDownload / File: emd_11455.map.gz / Format: CCP4 / Size: 441.8 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
Voxel sizeX=Y=Z: 6.8 Å
Density
Minimum - Maximum-118.0 - 89.0
Average (Standard dev.)0.6202356 (±6.561323)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin13017-16
Dimensions928960260
Spacing960928260
CellA: 6528.0 Å / B: 6310.4004 Å / C: 1768.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z6.86.86.8
M x/y/z960928260
origin x/y/z0.0000.0000.000
length x/y/z6528.0006310.4001768.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS17130-16
NC/NR/NS960928260
D min/max/mean-118.00089.0000.620

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Supplemental data

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Sample components

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Entire : VAP-A and OSBP

EntireName: VAP-A and OSBP
Components
  • Complex: VAP-A and OSBP

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Supramolecule #1: VAP-A and OSBP

SupramoleculeName: VAP-A and OSBP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
Component:
ConcentrationFormulaName
50.0 mMC8H18N2O4S4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
120.0 mMC2H3KO2Potassium acetate

Details: 50 mM HEPES pH 7.4 120 mM potassium acetate
GridModel: Homemade / Support film - Material: CARBON / Support film - topology: LACEY
VitrificationCryogen name: ETHANE / Chamber humidity: 98 % / Chamber temperature: 21 K / Instrument: LEICA PLUNGER
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: home made / Diameter: 6 nm

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 2 / Average electron dose: 3.5 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFPHASEFLIP
Final reconstructionAlgorithm: BACK PROJECTION / Software - Name: eTomo / Number images used: 41

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