[English] 日本語
Yorodumi
- EMDB-53267: Cryo-EM structure of TTYH3 in GDN after incubation with ApoE, map1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-53267
TitleCryo-EM structure of TTYH3 in GDN after incubation with ApoE, map1
Map dataTTYH3 low resolution class
Sample
  • Complex: TTYH3 dimer purified in GDN
    • Protein or peptide: TTYH3 homodimer
KeywordsMembrane protein / lipid interactions
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.59 Å
AuthorsSukalskaia A / Pugnetti A / Dutzler R / Plochberger B / Weber F / Karner A
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: To Be Published
Title: Interactions between TTYH2 and ApoE facilitate endosomal lipid transfer
Authors: Sukalskaia A / Pugnetti AS / Dutzler R / Plochberger B / Weber F / Karner A
History
DepositionMar 26, 2025-
Header (metadata) releaseMay 21, 2025-
Map releaseMay 21, 2025-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_53267.png

Downloads & links

-
Map

FileDownload / File: emd_53267.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTTYH3 low resolution class
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: 0.1
Minimum - Maximum-0.27719706 - 0.5781576
Average (Standard dev.)-0.00007095837 (±0.018420355)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Half map: halfmap1

Fileemd_53267_half_map_1.map
Annotationhalfmap1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: halfmap2

Fileemd_53267_half_map_2.map
Annotationhalfmap2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : TTYH3 dimer purified in GDN

EntireName: TTYH3 dimer purified in GDN
Components
  • Complex: TTYH3 dimer purified in GDN
    • Protein or peptide: TTYH3 homodimer

-
Supramolecule #1: TTYH3 dimer purified in GDN

SupramoleculeName: TTYH3 dimer purified in GDN / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 130 KDa

-
Macromolecule #1: TTYH3 homodimer

MacromoleculeName: TTYH3 homodimer / type: protein_or_peptide / ID: 1 / Details: contains C-terminal Myc-tag followed by SBP-tag / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSAGVSYAAP WWVSLLHRLP HFDLSWEATS SQFRPEDTDY QQALLLLGAA ALACLALDLL FLLFYSFWLC CRRRKSEEHL DADCCCTAWC VIIATLVCSA GIAVGFYGNG ETSDGIHRAT YSLRHANRTV AGVQDRVWDT AVGLNHTAEP SLQTLERQLA GRPEPLRAVQ ...String:
MSAGVSYAAP WWVSLLHRLP HFDLSWEATS SQFRPEDTDY QQALLLLGAA ALACLALDLL FLLFYSFWLC CRRRKSEEHL DADCCCTAWC VIIATLVCSA GIAVGFYGNG ETSDGIHRAT YSLRHANRTV AGVQDRVWDT AVGLNHTAEP SLQTLERQLA GRPEPLRAVQ RLQGLLETLL GYTAAIPFWR NTAVSLEVLA EQVDLYDWYR WLGYLGLLLL DVIICLLVLV GLIRSSKGIL VGVCLLGVLA LVISWGALGL ELAVSVGSSD FCVDPDAYVT KMVEEYSVLS GDILQYYLAC SPRAANPFQQ KLSGSHKALV EMQDVVAELL RTVPWEQPAT KDPLLRVQEV LNGTEVNLQH LTALVDCRSL HLDYVQALTG FCYDGVEGLI YLALFSFVTA LMFSSIVCSV PHTWQQKRGP DEDGEEEAAP GPRQAHDSLY RVHMPSLYSC GSSYGSETSI PAAAHTVSNA PVTEYMSQNA NFQNPRCENT PLIGRESPPP SYTSSMRAKY LATSQPRPDS SGSHALEVLF QGPQGTEQKL ISEEDLRGAS MDEKTTGWRG GHVVEGLAGE LEQLRARLEH HPQGQREP

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.5 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
200.0 mMNaClsodium chloride
10.0 mMHepeshepes
50.0 mMGDNglycodiosgenin
VitrificationCryogen name: NITROGEN / Instrument: FEI VITROBOT MARK IV
DetailsThis sample contained TTYH3 mixed with apolipoprotein E. No complex formation between the two proteins was detected. The resulting maps display only TTYH3 density.

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 68.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

+
Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.59 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 5526
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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