[English] 日本語
Yorodumi
- EMDB-52170: Structure of the Ist2 TMEM16 homology domain in the detergent GDN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-52170
TitleStructure of the Ist2 TMEM16 homology domain in the detergent GDN
Map dataStructure of the N-terminal domain encompassing residues 1-716 of Ist2 purified from S.cerevisiae
Sample
  • Complex: Homodimer of N-terminal domain of Ist2
    • Protein or peptide: Increased sodium tolerance protein 2
KeywordsTMEM16 proteins / lipid scramblase / lipid transport / membrane contact sites / tethering protein / MEMBRANE PROTEIN
Function / homology
Function and homology information


Stimuli-sensing channels / cellular bud membrane / endoplasmic reticulum membrane organization / regulation of phosphatidylinositol dephosphorylation / cortical endoplasmic reticulum / chloride channel activity / Neutrophil degranulation / chloride transmembrane transport / cell periphery / protein localization to plasma membrane ...Stimuli-sensing channels / cellular bud membrane / endoplasmic reticulum membrane organization / regulation of phosphatidylinositol dephosphorylation / cortical endoplasmic reticulum / chloride channel activity / Neutrophil degranulation / chloride transmembrane transport / cell periphery / protein localization to plasma membrane / lipid binding / plasma membrane
Similarity search - Function
Anoctamin / : / Calcium-activated chloride channel
Similarity search - Domain/homology
Increased sodium tolerance protein 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsArndt M / Dutzler R
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation215236 Switzerland
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Structural basis for lipid transport at membrane contact sites by the IST2-OSH6 complex.
Authors: Melanie Arndt / Angela Schweri / Raimund Dutzler /
Abstract: Membrane contact sites are hubs for interorganellar lipid transport within eukaryotic cells. As a principal tether bridging the endoplasmic reticulum (ER) and the plasma membrane in Saccharomyces ...Membrane contact sites are hubs for interorganellar lipid transport within eukaryotic cells. As a principal tether bridging the endoplasmic reticulum (ER) and the plasma membrane in Saccharomyces cerevisiae, the protein IST2 has a major role during lipid transport between both compartments. Here, we show a comprehensive investigation elucidating the structural and mechanistic properties of IST2 and its interaction with the soluble lipid transfer protein OSH6. The ER-embedded transmembrane domain of IST2 is homologous to the TMEM16 family and acts as a constitutively active lipid scramblase. The extended C terminus binds to the plasma membrane and the phosphatidylserine-phosphatidylinositol 4-phosphate exchanger OSH6. Through cellular growth assays and biochemical and structural studies, we characterized the interaction between both proteins and show that OSH6 remains associated with IST2 during lipid shuttling between membranes. These results highlight the role of the IST2-OSH6 complex in lipid trafficking and offer initial insights into the relevance of scramblases for carrier-like lipid transport mechanisms.
History
DepositionNov 21, 2024-
Header (metadata) releaseSep 3, 2025-
Map releaseSep 3, 2025-
UpdateSep 3, 2025-
Current statusSep 3, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_52170.png

Downloads & links

-
Map

FileDownload / File: emd_52170.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of the N-terminal domain encompassing residues 1-716 of Ist2 purified from S.cerevisiae
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
0.65 Å/pix.
x 480 pix.
= 312.48 Å		0.65 Å/pix.
x 480 pix.
= 312.48 Å		0.65 Å/pix.
x 480 pix.
= 312.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.651 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.075
Minimum - Maximum-0.39402366 - 0.59848034
Average (Standard dev.)-0.0003021424 (±0.01072285)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 312.48 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Half-map B of Structure of the N-terminal domain...

Fileemd_52170_half_map_1.map
AnnotationHalf-map B of Structure of the N-terminal domain encompassing residues 1-716 of Ist2 purified from S.cerevisiae
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half-map A of Structure of the N-terminal domain...

Fileemd_52170_half_map_2.map
AnnotationHalf-map A of Structure of the N-terminal domain encompassing residues 1-716 of Ist2 purified from S.cerevisiae
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Homodimer of N-terminal domain of Ist2

EntireName: Homodimer of N-terminal domain of Ist2
Components
  • Complex: Homodimer of N-terminal domain of Ist2
    • Protein or peptide: Increased sodium tolerance protein 2

-
Supramolecule #1: Homodimer of N-terminal domain of Ist2

SupramoleculeName: Homodimer of N-terminal domain of Ist2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

-
Macromolecule #1: Increased sodium tolerance protein 2

MacromoleculeName: Increased sodium tolerance protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 87.777375 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MDEKTTGWRG GHVVEGLAGE LEQLRARLEH HPQGQREPEQ KLISEEDLGT LEVLFQGPSS QTITSLDPNC VIVFNKTSSA NEKSLNVEF KRLNIHSIIE PGHDLQTSYA FIRIHQDNAK PLFSFLQNLD FIESIIPYHD TELSDDLHKL ISISKSKILE A PKQYELYN ...String:
MDEKTTGWRG GHVVEGLAGE LEQLRARLEH HPQGQREPEQ KLISEEDLGT LEVLFQGPSS QTITSLDPNC VIVFNKTSSA NEKSLNVEF KRLNIHSIIE PGHDLQTSYA FIRIHQDNAK PLFSFLQNLD FIESIIPYHD TELSDDLHKL ISISKSKILE A PKQYELYN LSNLTNNPKQ SLYFAFLQNY IKWLIPFSFF GLSIRFLSNF TYEFNSTYSL FAILWTLSFT AFWLYKYEPF WS DRLSKYS SFSTIEFLQD KQKAQKKASS VIMLKKCCFI PVALLFGAIL LSFQLYCFAL EIFIKQIYNG PMISILSFLP TIL ICTFTP VLTVIYNKYF VEPMTKWENH SSVVNAKKSK EAKNFVIIFL SSYVPLLITL FLYLPMGHLL TAEIRTKVFN AFSI LARLP THDSDFIIDT KRYEDQFFYF IVINQLIQFS MENFVPSLVS IAQQKINGPN PNFVKAESEI GKAQLSSSDM KIWSK VKSY QTDPWGATFD LDANFKKLLL QFGYLVMFST IWPLAPFICL IVNLIVYQVD LRKAVLYSKP EYFPFPIYDK PSSVSN TQK LTVGLWNSVL VMFSILGCVI TATLTYMYQS CNIPGVGAHT SIHTNKAWYL ANPINHSWIN IVLYAVFIEH VSVAIFF LF SSILKSSHDD VANGIVPKHV VNVQNPPKQE VFEKIPSPEF NSNNEKELVQ RKGSANEKLH QELGEKQPAS SANGYEAH A ATHANNDPSS LSSASSPSLS SSSSSSKTGV VKAVDNDTAG SAGKKPLATE STEA

UniProtKB: Increased sodium tolerance protein 2

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2.56 mg/mL
BufferpH: 7.6
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 4 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 62.43 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
In silico model: ab-initio reconstruction calculated in cryoSPARC
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 400925
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

1-v4


Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL
Output model

PDB-9hhe:
Structure of the Ist2 TMEM16 homology domain in the detergent GDN

+
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