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- EMDB-53291: TTYH2 in complex with sybody 1 in cell-derived vesicles -

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Basic information

Entry
Database: EMDB / ID: EMD-53291
TitleTTYH2 in complex with sybody 1 in cell-derived vesicles
Map data
Sample
  • Complex: TTYH2 in complex with a synthetic nanobody residing in cell-derived vesicles
    • Complex: Sybody 1
      • Protein or peptide: Sybody 1
    • Complex: TTYH2 homodimer
      • Protein or peptide: TTYH2 homodimer
Keywordsmembrane protein / synthetic nanobody / native vesicles
Biological speciessynthetic construct (others) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.23 Å
AuthorsSukalskaia A / Dutzler R / Pugnetti A / Karner A / Weber F / Plochberger B
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: To Be Published
Title: Interactions between TTYH2 and ApoE facilitate endosomal lipid transfer
Authors: Sukalskaia A / Dutzler R / Pugnetti A / Karner A / Weber F / Plochberger B
History
DepositionMar 31, 2025-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53291.png

Downloads & links

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Map

FileDownload / File: emd_53291.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: 0.172
Minimum - Maximum-0.7652308 - 1.0959227
Average (Standard dev.)0.009402283 (±0.056767464)
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_53291_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_53291_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 in complex with a synthetic nanobody residing in cell-deriv...

EntireName: TTYH2 in complex with a synthetic nanobody residing in cell-derived vesicles
Components
  • Complex: TTYH2 in complex with a synthetic nanobody residing in cell-derived vesicles
    • Complex: Sybody 1
      • Protein or peptide: Sybody 1
    • Complex: TTYH2 homodimer
      • Protein or peptide: TTYH2 homodimer

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Supramolecule #1: TTYH2 in complex with a synthetic nanobody residing in cell-deriv...

SupramoleculeName: TTYH2 in complex with a synthetic nanobody residing in cell-derived vesicles
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 149 KDa

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Supramolecule #2: Sybody 1

SupramoleculeName: Sybody 1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: synthetic construct (others)

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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 followed 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: Sybody 1

MacromoleculeName: Sybody 1 / type: protein_or_peptide / ID: 2 / Details: contains a C-terminal Myc-tag followed by His-tag / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: Escherichia coli MC1061 (bacteria)
SequenceString:
MAGSSSQVQL VESGGGLVQA GGSLRLSCAA SGFPVTNDSM HWYRQAPGKE REWVAAIASQ GRGTAYADSV KGRFTISRDN AKSTVYLQMN SLKPEDTAVY YCNVKDYGYD LQWYDYWGQG TQVTVSAGRA GEQKLISEED LNSAVDHHHH HH

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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: 69.33 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: 8.23 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 31014
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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