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- EMDB-53289: TTYH2 in complex with delipidated ApoE -

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Basic information

Entry
Database: EMDB / ID: EMD-53289
TitleTTYH2 in complex with delipidated ApoE
Map data
Sample
  • Complex: TTYH2 homodimer in complex with delipidated ApoE
    • Complex: ApoE delipidated
      • Protein or peptide: ApoE delipidated
    • Complex: TTYH2 homodimer
      • Protein or peptide: TTYH2 homodimer
KeywordsMembrane protein / lipid interactions / apolipoprotein
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.02 Å
AuthorsSukalskaia A / Dutzler R / Plochberger B / Pugnetti A / Karner A / Weber F
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: To Be Published
Title: TTYH2 in complex with lipidated ApoE
Authors: Sukalskaia A / Dutzler R / Plochberger B / Pugnetti A / Karner A / Weber F
History
DepositionMar 31, 2025-
Header (metadata) releaseMay 21, 2025-
Map releaseMay 21, 2025-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53289.png

Downloads & links

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Map

FileDownload / File: emd_53289.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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: 0.103
Minimum - Maximum-0.46666703 - 0.77393806
Average (Standard dev.)0.00009843453 (±0.020436473)
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: #1

Fileemd_53289_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_53289_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 : TTYH2 homodimer in complex with delipidated ApoE

EntireName: TTYH2 homodimer in complex with delipidated ApoE
Components
  • Complex: TTYH2 homodimer in complex with delipidated ApoE
    • Complex: ApoE delipidated
      • Protein or peptide: ApoE delipidated
    • Complex: TTYH2 homodimer
      • Protein or peptide: TTYH2 homodimer

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Supramolecule #1: TTYH2 homodimer in complex with delipidated ApoE

SupramoleculeName: TTYH2 homodimer in complex with delipidated ApoE / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 132 KDa

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Supramolecule #2: ApoE delipidated

SupramoleculeName: ApoE delipidated / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: TTYH2 homodimer

SupramoleculeName: TTYH2 homodimer / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: TTYH2 homodimer

MacromoleculeName: TTYH2 homodimer / type: protein_or_peptide / ID: 1 / Details: contains a C-terminal Myc-tag followd by SBP-tag / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSQAARVDYI APWWVVWLHS VPHVGLRLQP VNSTFSPGDE SYQESLLFLG LVAAVCLGLN LIFLVAYLVC ACHCRRDDAV QTKQHHSCCI TWTAVVAGLI CCAAVGVGFY GNSETNDGAY QLMYSLDDAN HTFSGIDALV SGTTQKMKVD LEQHLARLSE IFAARGDYLQ ...String:
MSQAARVDYI APWWVVWLHS VPHVGLRLQP VNSTFSPGDE SYQESLLFLG LVAAVCLGLN LIFLVAYLVC ACHCRRDDAV QTKQHHSCCI TWTAVVAGLI CCAAVGVGFY GNSETNDGAY QLMYSLDDAN HTFSGIDALV SGTTQKMKVD LEQHLARLSE IFAARGDYLQ TLKFIQQMAG SVVVQLSGLP VWREVTMELT KLSDQTGYVE YYRWLSYLLL FILDLVICLI ACLGLAKRSK CLLASMLCCG ALSLLLSWAS LAADGSAAVA TSDFCVAPDT FILNVTEGQI STEVTRYYLY CSQSGSSPFQ QTLTTFQRAL TTMQIQVAGL LQFAVPLFST AEEDLLAIQL LLNSSESSLH QLTAMVDCRG LHKDYLDALA GICYDGLQGL LYLGLFSFLA ALAFSTMICA GPRAWKHFTT RNRDYDDIDD DDPFNPQAWR MAAHSPPRGQ LHSFCSYSSG LGSQTSLQPP AQTISNAPVS EYMNQAMLFG RNPRYENVPL IGRASPPPTY SPSMRATYLS VADEHLRHYG NQFPAALEVL FQGPQGTEQK LISEEDLRGA SMDEKTTGWR GGHVVEGLAG ELEQLRARLE HHPQGQREP

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Macromolecule #2: ApoE delipidated

MacromoleculeName: ApoE delipidated / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
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
0.05 mMGDNglycodiosgenin
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: 59.6 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: 4.02 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 59807
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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