[English] 日本語
Yorodumi
- EMDB-13201: Cryo-EM structure of human TTYH2 in lipid nanodiscs -

+
Open data


ID or keywords:

Loading...

-
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
Function / homologyvolume-sensitive chloride channel activity / Tweety / Tweety / intracellularly calcium-gated chloride channel activity / chloride channel complex / Stimuli-sensing channels / plasma membrane / Protein tweety homolog 2
Function and homology information
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-
UpdateSep 8, 2021-
Current statusSep 8, 2021Processing site: PDBe / Status: Released

-
Structure visualization

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

emd_13201.png

Downloads & links

-
Map

FileDownload / File: emd_13201.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.302 Å
Density
Contour LevelBy AUTHOR: 0.0285 / Movie #1: 0.0285
Minimum - Maximum-0.15192622 - 0.21822394
Average (Standard dev.)-4.0976506e-06 (±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

-
Supplemental data

-
Mask #1

Fileemd_13201_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_13201_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_13201_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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

-
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)
Recombinant expressionOrganism: Homo sapiens (human)
Molecular weightTheoretical: 119 KDa

-
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

-
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 / N-Acetylglucosamine

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMC8H18N2O4SHEPES
200.0 mMNaClSodium chloridesodium chloride
2.0 mMC10H16N2O8EDTAEthylenediaminetetraacetic acid
50.0 uMC56H92O25GDN
VitrificationCryogen name: ETHANE-PROPANE / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

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

-
Image processing

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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more