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- EMDB-41831: Gradient-fixed lipidated recombinant apolipoprotein E4 -

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Basic information

Entry
Database: EMDB / ID: EMD-41831
TitleGradient-fixed lipidated recombinant apolipoprotein E4
Map dataGradient-fixed lipidated recombinant apolipoprotein E4
Sample
  • Complex: Gradient fixed lipidated recombinant apolipoprotein E4 in complex with monoclonal anti-ApoE F(ab')2 fragment
KeywordsApolipoprotien E / ApoE / Lipoprotein / LIPID BINDING PROTEIN
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.71 Å
AuthorsStrickland MR / Rau M / Summers B / Basore K / Wulf II J / Jiang H / Chen Y / Ulrich JD / Randolph GJ / Zhang R ...Strickland MR / Rau M / Summers B / Basore K / Wulf II J / Jiang H / Chen Y / Ulrich JD / Randolph GJ / Zhang R / Fitzpatrick JAJ / Cashikar AG / Holtzman DM
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)T32AG058518 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)RF1NS090934 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)1U19AG069701 United States
National Science Foundation (NSF, United States)DGE-1745038 United States
Other private United States
CitationJournal: Neuron / Year: 2024
Title: Apolipoprotein E secreted by astrocytes forms antiparallel dimers in discoidal lipoproteins.
Authors: Michael R Strickland / Michael J Rau / Brock Summers / Katherine Basore / John Wulf / Hong Jiang / Yun Chen / Jason D Ulrich / Gwendalyn J Randolph / Rui Zhang / James A J Fitzpatrick / Anil ...Authors: Michael R Strickland / Michael J Rau / Brock Summers / Katherine Basore / John Wulf / Hong Jiang / Yun Chen / Jason D Ulrich / Gwendalyn J Randolph / Rui Zhang / James A J Fitzpatrick / Anil G Cashikar / David M Holtzman /
Abstract: The Apolipoprotein E gene (APOE) is of great interest due to its role as a risk factor for late-onset Alzheimer's disease. ApoE is secreted by astrocytes in the central nervous system in high-density ...The Apolipoprotein E gene (APOE) is of great interest due to its role as a risk factor for late-onset Alzheimer's disease. ApoE is secreted by astrocytes in the central nervous system in high-density lipoprotein (HDL)-like lipoproteins. Structural models of lipidated ApoE of high resolution could aid in a mechanistic understanding of how ApoE functions in health and disease. Using monoclonal Fab and F(ab') fragments, we characterize the structure of lipidated ApoE on astrocyte-secreted lipoproteins. Our results provide support for the "double-belt" model of ApoE in nascent discoidal HDL-like lipoproteins, where two ApoE proteins wrap around the nanodisc in an antiparallel conformation. We further show that lipidated, recombinant ApoE accurately models astrocyte-secreted ApoE lipoproteins. Cryogenic electron microscopy of recombinant lipidated ApoE further supports ApoE adopting antiparallel dimers in nascent discoidal lipoproteins.
History
DepositionSep 3, 2023-
Header (metadata) releaseJan 24, 2024-
Map releaseJan 24, 2024-
UpdateApr 17, 2024-
Current statusApr 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41831.png

Downloads & links

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Map

FileDownload / File: emd_41831.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGradient-fixed lipidated recombinant apolipoprotein E4
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 600 pix.
= 556.8 Å		0.93 Å/pix.
x 600 pix.
= 556.8 Å		0.93 Å/pix.
x 600 pix.
= 556.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.928 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0886
Minimum - Maximum-0.58472586 - 2.431171
Average (Standard dev.)-0.00046778852 (±0.04148413)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 556.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map 1

Fileemd_41831_half_map_1.map
AnnotationHalf Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 2

Fileemd_41831_half_map_2.map
AnnotationHalf Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Gradient fixed lipidated recombinant apolipoprotein E4 in complex...

EntireName: Gradient fixed lipidated recombinant apolipoprotein E4 in complex with monoclonal anti-ApoE F(ab')2 fragment
Components
  • Complex: Gradient fixed lipidated recombinant apolipoprotein E4 in complex with monoclonal anti-ApoE F(ab')2 fragment

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Supramolecule #1: Gradient fixed lipidated recombinant apolipoprotein E4 in complex...

SupramoleculeName: Gradient fixed lipidated recombinant apolipoprotein E4 in complex with monoclonal anti-ApoE F(ab')2 fragment
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 182 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

BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: GRAPHENE OXIDE / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 52.8 e/Å2

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.71 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 51037
FSC plot (resolution estimation)

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