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- EMDB-51108: Cryo-EM structure of TTYH2 in complex with lipids in GDN -

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Basic information

Entry
Database: EMDB / ID: EMD-51108
TitleCryo-EM structure of TTYH2 in complex with lipids in GDN
Map data
Sample
  • Complex: TTYH2 purified in GDN with lipids
    • Protein or peptide: Protein tweety homolog 2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: DIUNDECYL PHOSPHATIDYL CHOLINE
  • Ligand: CHOLESTEROL
  • Ligand: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
Keywordscomplex / sybody / nanobody / TTYH2 / MEMBRANE PROTEIN
Function / homology
Function and homology information


volume-sensitive chloride channel activity / L-glutamate transmembrane transport / intracellularly calcium-gated chloride channel activity / chloride channel complex / Stimuli-sensing channels / calcium ion binding / plasma membrane
Similarity search - Function
Protein tweety homolog 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.74 Å
AuthorsSukalskaia A / Weber F / Plochberger B / Dutzler R
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: To Be Published
Title: TTYH2 with lipids in GDN
Authors: Sukalskaia A / Weber F / Plochberger B / Dutzler R
History
DepositionJul 19, 2024-
Header (metadata) releaseMay 21, 2025-
Map releaseMay 21, 2025-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51108.png

Downloads & links

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Map

FileDownload / File: emd_51108.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: 0.271
Minimum - Maximum-3.0693817 - 4.317229
Average (Standard dev.)-0.0004852107 (±0.069372974)
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: #2

Fileemd_51108_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_51108_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 purified in GDN with lipids

EntireName: TTYH2 purified in GDN with lipids
Components
  • Complex: TTYH2 purified in GDN with lipids
    • Protein or peptide: Protein tweety homolog 2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: DIUNDECYL PHOSPHATIDYL CHOLINE
  • Ligand: CHOLESTEROL
  • Ligand: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

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Supramolecule #1: TTYH2 purified in GDN with lipids

SupramoleculeName: TTYH2 purified in GDN with lipids / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 66 KDa

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Macromolecule #1: Protein tweety homolog 2

MacromoleculeName: Protein tweety homolog 2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 66.000039 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSQAARVDYI APWWVVWLHS VPHVGLRLQP VNSTFSPGDE SYQESLLFLG LVAAVCLGLN LIFLVAYLVC ACHCRRDDAV QTKQHHSCC ITWTAVVAGL ICCAAVGVGF YGNSETNDGA YQLMYSLDDA NHTFSGIDAL VSGTTQKMKV DLEQHLARLS E IFAARGDY ...String:
MSQAARVDYI APWWVVWLHS VPHVGLRLQP VNSTFSPGDE SYQESLLFLG LVAAVCLGLN LIFLVAYLVC ACHCRRDDAV QTKQHHSCC ITWTAVVAGL ICCAAVGVGF YGNSETNDGA YQLMYSLDDA NHTFSGIDAL VSGTTQKMKV DLEQHLARLS E IFAARGDY LQTLKFIQQM AGSVVVQLSG LPVWREVTME LTKLSDQTGY VEYYRWLSYL LLFILDLVIC LIACLGLAKR SK CLLASML CCGALSLLLS WASLAADGSA AVATSDFCVA PDTFILNVTE GQISTEVTRY YLYCSQSGSS PFQQTLTTFQ RAL TTMQIQ VAGLLQFAVP LFSTAEEDLL AIQLLLNSSE SSLHQLTAMV DCRGLHKDYL DALAGICYDG LQGLLYLGLF SFLA ALAFS TMICAGPRAW KHFTTRNRDY DDIDDDDPFN PQAWRMAAHS PPRGQLHSFC SYSSGLGSQT SLQPPAQTIS NAPVS EYMN QAMLFGRNPR YENVPLIGRA SPPPTYSPSM RATYLSVADE HLRHYGNQFP AALEVLFQGP QGTEQKLISE EDLRGA SMD EKTTGWRGGH VVEGLAGELE QLRARLEHHP QGQREP

UniProtKB: Protein tweety homolog 2

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #4: DIUNDECYL PHOSPHATIDYL CHOLINE

MacromoleculeName: DIUNDECYL PHOSPHATIDYL CHOLINE / type: ligand / ID: 4 / Number of copies: 17 / Formula: PLC
Molecular weightTheoretical: 622.834 Da
Chemical component information

ChemComp-PLC:
DIUNDECYL PHOSPHATIDYL CHOLINE / phospholipid*YM

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Macromolecule #5: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 5 / Number of copies: 6 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #6: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 6 / Number of copies: 3 / Formula: CPL
Molecular weightTheoretical: 758.06 Da
Chemical component information

ChemComp-CPL:
1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM

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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
50.0 uMGDNglycodiosgenin
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 63.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination 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: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.74 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 2192921
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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