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- EMDB-53267: Cryo-EM structure of TTYH3 in GDN after incubation with ApoE, map1 -

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Basic information

Entry
Database: EMDB / ID: EMD-53267
TitleCryo-EM structure of TTYH3 in GDN after incubation with ApoE, map1
Map dataTTYH3 low resolution class
Sample
  • Complex: TTYH3 dimer purified in GDN
    • Protein or peptide: TTYH3 homodimer
KeywordsMembrane protein / lipid interactions
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.59 Å
AuthorsSukalskaia A / Pugnetti A / Dutzler R / Plochberger B / Weber F / Karner A
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-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53267.png

Downloads & links

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Map

FileDownload / File: emd_53267.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTTYH3 low resolution class
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 220 pix.
= 286.44 Å		1.3 Å/pix.
x 220 pix.
= 286.44 Å		1.3 Å/pix.
x 220 pix.
= 286.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.302 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.27719706 - 0.5781576
Average (Standard dev.)-0.00007095837 (±0.018420355)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 286.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: halfmap1

Fileemd_53267_half_map_1.map
Annotationhalfmap1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halfmap2

Fileemd_53267_half_map_2.map
Annotationhalfmap2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : TTYH3 dimer purified in GDN

EntireName: TTYH3 dimer purified in GDN
Components
  • Complex: TTYH3 dimer purified in GDN
    • Protein or peptide: TTYH3 homodimer

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Supramolecule #1: TTYH3 dimer purified in GDN

SupramoleculeName: TTYH3 dimer purified in GDN / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 130 KDa

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Macromolecule #1: TTYH3 homodimer

MacromoleculeName: TTYH3 homodimer / type: protein_or_peptide / ID: 1 / Details: contains C-terminal Myc-tag followed by SBP-tag / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSAGVSYAAP WWVSLLHRLP HFDLSWEATS SQFRPEDTDY QQALLLLGAA ALACLALDLL FLLFYSFWLC CRRRKSEEHL DADCCCTAWC VIIATLVCSA GIAVGFYGNG ETSDGIHRAT YSLRHANRTV AGVQDRVWDT AVGLNHTAEP SLQTLERQLA GRPEPLRAVQ ...String:
MSAGVSYAAP WWVSLLHRLP HFDLSWEATS SQFRPEDTDY QQALLLLGAA ALACLALDLL FLLFYSFWLC CRRRKSEEHL DADCCCTAWC VIIATLVCSA GIAVGFYGNG ETSDGIHRAT YSLRHANRTV AGVQDRVWDT AVGLNHTAEP SLQTLERQLA GRPEPLRAVQ RLQGLLETLL GYTAAIPFWR NTAVSLEVLA EQVDLYDWYR WLGYLGLLLL DVIICLLVLV GLIRSSKGIL VGVCLLGVLA LVISWGALGL ELAVSVGSSD FCVDPDAYVT KMVEEYSVLS GDILQYYLAC SPRAANPFQQ KLSGSHKALV EMQDVVAELL RTVPWEQPAT KDPLLRVQEV LNGTEVNLQH LTALVDCRSL HLDYVQALTG FCYDGVEGLI YLALFSFVTA LMFSSIVCSV PHTWQQKRGP DEDGEEEAAP GPRQAHDSLY RVHMPSLYSC GSSYGSETSI PAAAHTVSNA PVTEYMSQNA NFQNPRCENT PLIGRESPPP SYTSSMRAKY LATSQPRPDS SGSHALEVLF QGPQGTEQKL ISEEDLRGAS MDEKTTGWRG GHVVEGLAGE LEQLRARLEH HPQGQREP

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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

Concentration1.5 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
200.0 mMNaClsodium chloride
10.0 mMHepeshepes
50.0 mMGDNglycodiosgenin
VitrificationCryogen name: NITROGEN / Instrument: FEI VITROBOT MARK IV
DetailsThis sample contained TTYH3 mixed with apolipoprotein E. No complex formation between the two proteins was detected. The resulting maps display only TTYH3 density.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 68.0 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: 7.59 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 5526
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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