[English] 日本語
Yorodumi
- EMDB-75606: Structure of cholesterol binding deficient human TM6SF1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-75606
TitleStructure of cholesterol binding deficient human TM6SF1
Map data
Sample
  • Organelle or cellular component: Structure of cholesterol binding deficient human TM6SF1
    • Protein or peptide: Transmembrane 6 superfamily member 1
KeywordsCholesterol binding protein / LIPID BINDING PROTEIN
Function / homology: / : / Transmembrane 6 superfamily member 2-like, transmembrane domain / EXPERA domain / EXPERA domain profile. / lysosomal membrane / Transmembrane 6 superfamily member 1
Function and homology information
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.37 Å
AuthorsHong S / Li X
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)NIH-R01DK090066 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: Structure and function of TM6SF1 reveals role in mTORC1 signaling.
Authors: Sen Hong / Liangjie Jia / Rong Wang / Nadia Elghobashi-Meinhardt / Helen H Hobbs / Xiaochun Li /
Abstract: The transmembrane 6 superfamily (TM6SF) comprises two members: TM6SF1, a ubiquitously expressed lysosomal membrane protein of unknown function, and TM6SF2, an endoplasmic reticulum protein required ...The transmembrane 6 superfamily (TM6SF) comprises two members: TM6SF1, a ubiquitously expressed lysosomal membrane protein of unknown function, and TM6SF2, an endoplasmic reticulum protein required for bulk lipidation of Apolipoprotein B-containing lipoproteins. Here, we used cryo-electron microscopy (cryo-EM) to determine the structure of human TM6SF1 at 2.9-Å resolution. TM6SF1 forms a polytopic homodimer, with each protomer comprising 10 transmembrane helices (TMs). TMs 1-6 form a pocket that accommodates a cholesterol molecule. Cell-based assays revealed that loss of TM6SF1 perturbs mTORC1 signaling, resulting in reduced phosphorylation of S6 kinase 1 and 4E-BP1 and constitutive activation of transcription factor EB (TFEB), and that cholesterol is required for these effects. Biochemical analyses support the model that TM6SF1 directly engages LAMTOR1, a component of Ragulator complex, in a cholesterol-dependent manner. Together, these findings identify TM6SF1 as a lysosomal cholesterol binding protein involved in regulating mTORC1 signaling.
History
DepositionFeb 16, 2026-
Header (metadata) releaseSep 9, 2026-
Map releaseSep 9, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_75606.png

Downloads & links

-
Map

FileDownload / File: emd_75606.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 350 pix.
= 291.9 Å		0.83 Å/pix.
x 350 pix.
= 291.9 Å		0.83 Å/pix.
x 350 pix.
= 291.9 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.834 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.27
Minimum - Maximum-0.30532774 - 0.98634785
Average (Standard dev.)0.0010418008 (±0.021439785)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 291.9 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_75606_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_75606_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Structure of cholesterol binding deficient human TM6SF1

EntireName: Structure of cholesterol binding deficient human TM6SF1
Components
  • Organelle or cellular component: Structure of cholesterol binding deficient human TM6SF1
    • Protein or peptide: Transmembrane 6 superfamily member 1

-
Supramolecule #1: Structure of cholesterol binding deficient human TM6SF1

SupramoleculeName: Structure of cholesterol binding deficient human TM6SF1
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.6 KDa

-
Macromolecule #1: Transmembrane 6 superfamily member 1

MacromoleculeName: Transmembrane 6 superfamily member 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.518703 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSASAATGVF VLSLSAIPVT YVFNHLAAQH DSWTIVGVAA LILFLVALLA RVLVKRKPPR DPLFYVYAVF GFTSVVALII GLEQDGIID GFMTHYLREG EPYLNTAYGH MICYWDGSAH YLMYLVMVAA IAWEETYRTI GLYWVGSIIM AVVVFVPGNI V GKYGTRIC ...String:
MSASAATGVF VLSLSAIPVT YVFNHLAAQH DSWTIVGVAA LILFLVALLA RVLVKRKPPR DPLFYVYAVF GFTSVVALII GLEQDGIID GFMTHYLREG EPYLNTAYGH MICYWDGSAH YLMYLVMVAA IAWEETYRTI GLYWVGSIIM AVVVFVPGNI V GKYGTRIC PAFFLSIPAT CLPVWAGFRI YNQPSENYNY PSKVIQEAQA KDLLRRPFDL MLVVCLLLAT GFCLFRGLIA LD CPSELCR LYTQFQEPYL KDPAAYPKIQ MLAYMFYSVP YFVTALYGLV VPGCSWMPDI TLIHAGGLAQ AQFSHIGASL HAR TAYVYR VPEEAKILFL ALNIAYGVLP QLLAYRCIYK PEFFIKTKAE EKVE

UniProtKB: Transmembrane 6 superfamily member 1

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration10 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: OTHER / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4) / Number images used: 163774
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
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