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- EMDB-51106: TTYH2 in complex with sybody 1 in GDN -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-51106
TitleTTYH2 in complex with sybody 1 in GDN
Map data
Sample
  • Complex: TTYH2 purified in GDN in complex with sybody 1
    • Complex: synthetic nanobody selected for binding TTYH2
      • Protein or peptide: sybody 1
    • Complex: TTYH2 purified in GDN
      • Protein or peptide: Protein tweety homolog 2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
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 speciesVicugna pacos (alpaca) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 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 in complex with sybody 1 in GDN
Authors: Sukalskaia A / Weber F / Plochberger B / Dutzler R
History
DepositionJul 19, 2024-
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_51106.png

Downloads & links

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Map

FileDownload / File: emd_51106.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: 0.11
Minimum - Maximum-0.67518103 - 1.2357175
Average (Standard dev.)-0.0009589014 (±0.02419575)
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_51106_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_51106_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 in complex with sybody 1

EntireName: TTYH2 purified in GDN in complex with sybody 1
Components
  • Complex: TTYH2 purified in GDN in complex with sybody 1
    • Complex: synthetic nanobody selected for binding TTYH2
      • Protein or peptide: sybody 1
    • Complex: TTYH2 purified in GDN
      • Protein or peptide: Protein tweety homolog 2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: TTYH2 purified in GDN in complex with sybody 1

SupramoleculeName: TTYH2 purified in GDN in complex with sybody 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Molecular weightTheoretical: 66 KDa

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Supramolecule #2: synthetic nanobody selected for binding TTYH2

SupramoleculeName: synthetic nanobody selected for binding TTYH2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Vicugna pacos (alpaca)

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Supramolecule #3: TTYH2 purified in GDN

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

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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 #2: sybody 1

MacromoleculeName: sybody 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vicugna pacos (alpaca)
Molecular weightTheoretical: 15.436077 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SQVQLVESGG GLVQAGGSLR LSCTASGFPV AFAQMKWYRQ APGKEREWVA AIWSMGNETT YADSVKGRFT ISRDNAKNTV YLQMNSLKP EDTAVYYCAV EVGYGYHGQG TQVTVSAGRA GEQKLISEED LNSAVDHHHH HH

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / 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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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: 68.48 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: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 75814
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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