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- EMDB-53273: ApoE lipoprotein disc, map2 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-53273
TitleApoE lipoprotein disc, map2
Map data
Sample
  • Complex: ApoE in complex with lipids
    • Protein or peptide: ApoE lipidated
Keywordslipoprotein / lipid transport / apolipoprotein
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.54 Å
AuthorsSukalskaia A / Dutzler R / Pugnetti AS / Karner A / Weber F / Plochberger B
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Nature / Year: 2025
Title: Interactions between TTYH2 and APOE facilitate endosomal lipid transfer.
Authors: Anastasiia Sukalskaia / Andreas Karner / Anna Pugnetti / Florian Weber / Birgit Plochberger / Raimund Dutzler /
Abstract: The Tweety homologues (TTYHs) constitute a family of eukaryotic membrane proteins that, on the basis of structural features, were recently proposed to contribute to lipid transfer between soluble ...The Tweety homologues (TTYHs) constitute a family of eukaryotic membrane proteins that, on the basis of structural features, were recently proposed to contribute to lipid transfer between soluble carriers and cellular membranes. However, in the absence of supporting data, this function was hypothetical. Here through pull-down of endogenous proteins, we identify APOE as the interaction partner of human TTYH2. Subcellular fractionation and immunocytochemistry assays showed that both proteins colocalize in endosomal compartments. Characterization of the specific interaction between APOE and TTYH2 through binding assays and structural studies enabled us to identify an epitope in an extended domain of TTYH2 that faces the endosomal lumen. Structures of complexes with APOE-containing lipoprotein particles revealed a binding mode that places lipids in a suitable position to facilitate their diffusion into the membrane. Moreover, in vitro studies revealed that lipid transfer is accelerated by TTYH2. Collectively, our findings indicate that TTYH2 has a role in the unloading of APOE-containing lipoproteins after they are endocytosed. These results define a new protein class that facilitates the extraction of lipids from and their insertion into cellular membranes. Although ubiquitous, this process could be of particular relevance in the brain, where APOE is involved in the transfer of lipids between astrocytes and neurons.
History
DepositionMar 26, 2025-
Header (metadata) releaseMay 21, 2025-
Map releaseMay 21, 2025-
UpdateAug 20, 2025-
Current statusAug 20, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53273.png

Downloads & links

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Map

FileDownload / File: emd_53273.map.gz / Format: CCP4 / Size: 5.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.6 Å/pix.
x 110 pix.
= 286.44 Å		2.6 Å/pix.
x 110 pix.
= 286.44 Å		2.6 Å/pix.
x 110 pix.
= 286.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.604 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0347
Minimum - Maximum-0.05770987 - 0.15158954
Average (Standard dev.)0.000140934 (±0.007524784)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions110110110
Spacing110110110
CellA=B=C: 286.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_53273_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_53273_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ApoE in complex with lipids

EntireName: ApoE in complex with lipids
Components
  • Complex: ApoE in complex with lipids
    • Protein or peptide: ApoE lipidated

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Supramolecule #1: ApoE in complex with lipids

SupramoleculeName: ApoE in complex with lipids / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 35 KDa

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Macromolecule #1: ApoE lipidated

MacromoleculeName: ApoE lipidated / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: PSKVEQAVET EPEPELRQQT EWQSGQRWEL ALGRFWDYLR WVQTLSEQVQ EELLSSQVTQ ELRALMDETM KELKAYKSEL EEQLTPVAEE TRARLSKELQ AAQARLGADM EDVCGRLVQY RGEVQAMLGQ STEELRVRLA SHLRKLRKRL LRDADDLQKR LAVYQAGARE ...String:
PSKVEQAVET EPEPELRQQT EWQSGQRWEL ALGRFWDYLR WVQTLSEQVQ EELLSSQVTQ ELRALMDETM KELKAYKSEL EEQLTPVAEE TRARLSKELQ AAQARLGADM EDVCGRLVQY RGEVQAMLGQ STEELRVRLA SHLRKLRKRL LRDADDLQKR LAVYQAGARE GAERGLSAIR ERLGPLVEQG RVRAATVGSL AGQPLQERAQ AWGERLRARM EEMGSRTRDR LDEVKEQVAE VRAKLEEQAQ QIRLQAEAFQ ARLKSWFEPL VEDMQRQWAG LVEKVQAAVG TSAAPVPSDN HA

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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
Component:
ConcentrationFormulaName
200.0 mMnaclsodium chloride
10.0 mMhepeshepes
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 61.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 9.54 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 74189
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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