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- EMDB-28044: Human ABCA7 in BPL/Ch nanodiscs (Map 2) -

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Basic information

Entry
Database: EMDB / ID: EMD-28044
TitleHuman ABCA7 in BPL/Ch nanodiscs (Map 2)
Map datahuman ABCA7 in BPL/Ch nanodiscs, alternative 3D class Map
Sample
  • Complex: Human ABCA7 in Porcine BPL/Ch/MSP1D1 nanodiscs
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsAlam A / Le LTM / Thompson JR
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)1R21AG069180 United States
CitationJournal: EMBO J / Year: 2023
Title: Cryo-EM structures of human ABCA7 provide insights into its phospholipid translocation mechanisms.
Authors: Le Thi My Le / James Robert Thompson / Sepehr Dehghani-Ghahnaviyeh / Shashank Pant / Phuoc Xuan Dang / Jarrod Bradley French / Takahisa Kanikeyo / Emad Tajkhorshid / Amer Alam /
Abstract: Phospholipid extrusion by ABC subfamily A (ABCA) exporters is central to cellular physiology, although the specifics of the underlying substrate interactions and transport mechanisms remain poorly ...Phospholipid extrusion by ABC subfamily A (ABCA) exporters is central to cellular physiology, although the specifics of the underlying substrate interactions and transport mechanisms remain poorly resolved at the molecular level. Here we report cryo-EM structures of lipid-embedded human ABCA7 in an open state and in a nucleotide-bound, closed state at resolutions between 3.6 and 4.0 Å. The former reveals an ordered patch of bilayer lipids traversing the transmembrane domain (TMD), while the latter reveals a lipid-free, closed TMD with a small extracellular opening. These structures offer a structural framework for both substrate entry and exit from the ABCA7 TMD and highlight conserved rigid-body motions that underlie the associated conformational transitions. Combined with functional analysis and molecular dynamics (MD) simulations, our data also shed light on lipid partitioning into the ABCA7 TMD and localized membrane perturbations that underlie ABCA7 function and have broader implications for other ABCA family transporters.
History
DepositionSep 6, 2022-
Header (metadata) releaseDec 21, 2022-
Map releaseDec 21, 2022-
UpdateFeb 15, 2023-
Current statusFeb 15, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28044.png

Downloads & links

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Map

FileDownload / File: emd_28044.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationhuman ABCA7 in BPL/Ch nanodiscs, alternative 3D class Map
Voxel sizeX=Y=Z: 0.895 Å
Density
Contour LevelBy AUTHOR: 0.006
Minimum - Maximum-0.06953939 - 0.12262618
Average (Standard dev.)5.5167075e-06 (±0.0023811436)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 343.68 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Refinement half map1

Fileemd_28044_half_map_1.map
AnnotationRefinement half map1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Refinement half map2

Fileemd_28044_half_map_2.map
AnnotationRefinement half map2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human ABCA7 in Porcine BPL/Ch/MSP1D1 nanodiscs

EntireName: Human ABCA7 in Porcine BPL/Ch/MSP1D1 nanodiscs
Components
  • Complex: Human ABCA7 in Porcine BPL/Ch/MSP1D1 nanodiscs

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Supramolecule #1: Human ABCA7 in Porcine BPL/Ch/MSP1D1 nanodiscs

SupramoleculeName: Human ABCA7 in Porcine BPL/Ch/MSP1D1 nanodiscs / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1
Details: Human ABCA7 recombinantly expressed in HEK293 TREX cell line and reconstituted in MSP1D1 nanodiscs comprising 4:1 mixture of Porcine Brain Polar Lipids:Cholesterol
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 234.35 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.5
Details: 25mM HEPES pH 7.5, 150mM NaCl, 5mM ATP gammaS, 10mM Magnesium Chloride
GridModel: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average exposure time: 60.0 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

9791

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1/4.0) / Number images used: 124114
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 1 / Software - Name: RELION (ver. 3.1)

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Atomic model buiding 1

Initial modelPDB ID:

6jbj

RefinementSpace: REAL / Protocol: AB INITIO MODEL

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