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- EMDB-13201: Cryo-EM structure of human TTYH2 in lipid nanodiscs -

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Basic information

Entry
Database: EMDB / ID: EMD-13201
TitleCryo-EM structure of human TTYH2 in lipid nanodiscs
Map data
Sample
  • Complex: TTYH2 in lipid nanodiscs
    • Protein or peptide: Protein tweety homolog 2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsMembrane protein / lipid metabolism / lipid transport
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: 3.92 Å
AuthorsSukalskaia A / Straub MS / Sawicka M / Deneka D / Dutzler R
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_163421 Switzerland
CitationJournal: Nat Commun / Year: 2021
Title: Cryo-EM structures of the TTYH family reveal a novel architecture for lipid interactions.
Authors: Anastasiia Sukalskaia / Monique S Straub / Dawid Deneka / Marta Sawicka / Raimund Dutzler /
Abstract: The Tweety homologs (TTYHs) are members of a conserved family of eukaryotic membrane proteins that are abundant in the brain. The three human paralogs were assigned to function as anion channels that ...The Tweety homologs (TTYHs) are members of a conserved family of eukaryotic membrane proteins that are abundant in the brain. The three human paralogs were assigned to function as anion channels that are either activated by Ca or cell swelling. To uncover their unknown architecture and its relationship to function, we have determined the structures of human TTYH1-3 by cryo-electron microscopy. All structures display equivalent features of a dimeric membrane protein that contains five transmembrane segments and an extended extracellular domain. As none of the proteins shows attributes reminiscent of an anion channel, we revisited functional experiments and did not find any indication of ion conduction. Instead, we find density in an extended hydrophobic pocket contained in the extracellular domain that emerges from the lipid bilayer, which suggests a role of TTYH proteins in the interaction with lipid-like compounds residing in the membrane.
History
DepositionJul 14, 2021-
Header (metadata) releaseAug 11, 2021-
Map releaseAug 11, 2021-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0285
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0285
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7p5m
  • Surface level: 0.0285
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13201.png

Downloads & links

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Map

FileDownload / File: emd_13201.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: 0.0285 / Movie #1: 0.0285
Minimum - Maximum-0.15192622 - 0.21822394
Average (Standard dev.)-0.0000040976506 (±0.0051271096)
SymmetrySpace group: 1
Details

EMDB XML:

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

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3021.3021.302
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z286.440286.440286.440
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ332332332
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS220220220
D min/max/mean-0.1520.218-0.000

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Supplemental data

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Mask #1

Fileemd_13201_msk_1.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Half map: #2

Fileemd_13201_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_13201_half_map_2.map
Projections & Slices
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Sample components

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Entire : TTYH2 in lipid nanodiscs

EntireName: TTYH2 in lipid nanodiscs
Components
  • Complex: TTYH2 in lipid nanodiscs
    • Protein or peptide: Protein tweety homolog 2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: TTYH2 in lipid nanodiscs

SupramoleculeName: TTYH2 in lipid nanodiscs / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 119 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: 59.573879 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SQAARVDYIA PWWVVWLHSV PHVGLRLQPV NSTFSPGDES YQESLLFLGL VAAVCLGLNL IFLVAYLVCA CHCRRDDAVQ TKQHHSCCI TWTAVVAGLI CCAAVGVGFY GNSETNDGAY QLMYSLDDAN HTFSGIDALV SGTTQKMKVD LEQHLARLSE I FAARGDYL ...String:
SQAARVDYIA PWWVVWLHSV PHVGLRLQPV NSTFSPGDES YQESLLFLGL VAAVCLGLNL IFLVAYLVCA CHCRRDDAVQ TKQHHSCCI TWTAVVAGLI CCAAVGVGFY GNSETNDGAY QLMYSLDDAN HTFSGIDALV SGTTQKMKVD LEQHLARLSE I FAARGDYL QTLKFIQQMA GSVVVQLSGL PVWREVTMEL TKLSDQTGYV EYYRWLSYLL LFILDLVICL IACLGLAKRS KC LLASMLC CGALSLLLSW ASLAADGSAA VATSDFCVAP DTFILNVTEG QISTEVTRYY LYCSQSGSSP FQQTLTTFQR ALT TMQIQV AGLLQFAVPL FSTAEEDLLA IQLLLNSSES SLHQLTAMVD CRGLHKDYLD ALAGICYDGL QGLLYLGLFS FLAA LAFST MICAGPRAWK HFTTRNRDYD DIDDDDPFNP QAWRMAAHSP PRGQLHSFCS YSSGLGSQTS LQPPAQTISN APVSE YMNQ AMLFGRNPRY ENVPLIGRAS PPPTYSPSMR ATYLSVADEH LRHYGNQFPA ALEVLFQ

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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMC8H18N2O4SHEPES
200.0 mMNaClsodium chloride
2.0 mMC10H16N2O8EDTA
50.0 uMC56H92O25GDN
VitrificationCryogen name: ETHANE-PROPANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 61.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.92 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 486362
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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