[English] 日本語
Yorodumi
- EMDB-53269: TTYH2 in complex with lipidated ApoE, dataset1 map2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-53269
TitleTTYH2 in complex with lipidated ApoE, dataset1 map2
Map data
Sample
  • Complex: TTYH2 homodimer in complex with lipidated ApoE
    • Complex: ApoE lipoprotein particle
      • Protein or peptide: ApoE lipidated
    • Complex: TTYH2 homodimer
      • Protein or peptide: TTYH2 homodimer
KeywordsMembrane protein / lipid interactions / apolipoprotein
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 13.0 Å
AuthorsSukalskaia A / Dutzler R / Plochberger B / Pugnetti AS / Karner A / Weber F
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: To Be Published
Title: TTYH2 in complex with lipidated ApoE
Authors: Sukalskaia A / Dutzler R / Plochberger B / Pugnetti AS / Karner A / Weber F
History
DepositionMar 26, 2025-
Header (metadata) releaseMay 21, 2025-
Map releaseMay 21, 2025-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_53269.png

Downloads & links

-
Map

FileDownload / File: emd_53269.map.gz / Format: CCP4 / Size: 5.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.6 Å/pix.
x 110 pix.
= 286.44 Å		2.6 Å/pix.
x 110 pix.
= 286.44 Å		2.6 Å/pix.
x 110 pix.
= 286.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.604 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0102
Minimum - Maximum-0.056847252 - 0.11978746
Average (Standard dev.)0.0004950425 (±0.00799246)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions110110110
Spacing110110110
CellA=B=C: 286.44 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_53269_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_53269_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : TTYH2 homodimer in complex with lipidated ApoE

EntireName: TTYH2 homodimer in complex with lipidated ApoE
Components
  • Complex: TTYH2 homodimer in complex with lipidated ApoE
    • Complex: ApoE lipoprotein particle
      • Protein or peptide: ApoE lipidated
    • Complex: TTYH2 homodimer
      • Protein or peptide: TTYH2 homodimer

-
Supramolecule #1: TTYH2 homodimer in complex with lipidated ApoE

SupramoleculeName: TTYH2 homodimer in complex with lipidated ApoE / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 132 KDa

-
Supramolecule #2: ApoE lipoprotein particle

SupramoleculeName: ApoE lipoprotein particle / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

-
Supramolecule #3: TTYH2 homodimer

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

-
Macromolecule #1: TTYH2 homodimer

MacromoleculeName: TTYH2 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)
SequenceString: MSQAARVDYI APWWVVWLHS VPHVGLRLQP VNSTFSPGDE SYQESLLFLG LVAAVCLGLN LIFLVAYLVC ACHCRRDDAV QTKQHHSCCI TWTAVVAGLI CCAAVGVGFY GNSETNDGAY QLMYSLDDAN HTFSGIDALV SGTTQKMKVD LEQHLARLSE IFAARGDYLQ ...String:
MSQAARVDYI APWWVVWLHS VPHVGLRLQP VNSTFSPGDE SYQESLLFLG LVAAVCLGLN LIFLVAYLVC ACHCRRDDAV QTKQHHSCCI TWTAVVAGLI CCAAVGVGFY GNSETNDGAY QLMYSLDDAN HTFSGIDALV SGTTQKMKVD LEQHLARLSE IFAARGDYLQ TLKFIQQMAG SVVVQLSGLP VWREVTMELT KLSDQTGYVE YYRWLSYLLL FILDLVICLI ACLGLAKRSK CLLASMLCCG ALSLLLSWAS LAADGSAAVA TSDFCVAPDT FILNVTEGQI STEVTRYYLY CSQSGSSPFQ QTLTTFQRAL TTMQIQVAGL LQFAVPLFST AEEDLLAIQL LLNSSESSLH QLTAMVDCRG LHKDYLDALA GICYDGLQGL LYLGLFSFLA ALAFSTMICA GPRAWKHFTT RNRDYDDIDD DDPFNPQAWR MAAHSPPRGQ LHSFCSYSSG LGSQTSLQPP AQTISNAPVS EYMNQAMLFG RNPRYENVPL IGRASPPPTY SPSMRATYLS VADEHLRHYG NQFPAALEVL FQGPQGTEQK LISEEDLRGA SMDEKTTGWR GGHVVEGLAG ELEQLRARLE HHPQGQREP

-
Macromolecule #2: ApoE lipidated

MacromoleculeName: ApoE lipidated / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: PSKVEQAVET EPEPELRQQT EWQSGQRWEL ALGRFWDYLR WVQTLSEQVQ EELLSSQVTQ ELRALMDETM KELKAYKSEL EEQLTPVAEE TRARLSKELQ AAQARLGADM EDVCGRLVQY RGEVQAMLGQ STEELRVRLA SHLRKLRKRL LRDADDLQKR LAVYQAGARE ...String:
PSKVEQAVET EPEPELRQQT EWQSGQRWEL ALGRFWDYLR WVQTLSEQVQ EELLSSQVTQ ELRALMDETM KELKAYKSEL EEQLTPVAEE TRARLSKELQ AAQARLGADM EDVCGRLVQY RGEVQAMLGQ STEELRVRLA SHLRKLRKRL LRDADDLQKR LAVYQAGARE GAERGLSAIR ERLGPLVEQG RVRAATVGSL AGQPLQERAQ AWGERLRARM EEMGSRTRDR LDEVKEQVAE VRAKLEEQAQ QIRLQAEAFQ ARLKSWFEPL VEDMQRQWAG LVEKVQAAVG TSAAPVPSDN HA

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
Component:
ConcentrationFormulaName
200.0 mMnaclsodium chloride
10.0 mMHEPEShepes
0.05 mMGDNglycodiosgenin
VitrificationCryogen name: NITROGEN

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 61.5 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: 13.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 17601
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