[English] 日本語
Yorodumi
- EMDB-63231: Cryo-EM structure of lumen facing G6PT1 in the apo state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-63231
TitleCryo-EM structure of lumen facing G6PT1 in the apo state
Map data
Sample
  • Complex: Cryo-EM structure of lumen facing G6PT1 in the apo state
    • Protein or peptide: Glucose-6-phosphate exchanger SLC37A4
  • Ligand: Lauryl Maltose Neopentyl Glycol
Keywordsprotein structure / STRUCTURAL PROTEIN / TRANSPORT PROTEIN
Function / homology
Function and homology information


glucose-6-phosphate transmembrane transporter activity / Glycogen storage disease type Ib (SLC37A4) / glucose-6-phosphate transport / glucose 6-phosphate:phosphate antiporter activity / Gluconeogenesis / phosphate ion transmembrane transport / gluconeogenesis / glucose metabolic process / glucose homeostasis / endoplasmic reticulum membrane ...glucose-6-phosphate transmembrane transporter activity / Glycogen storage disease type Ib (SLC37A4) / glucose-6-phosphate transport / glucose 6-phosphate:phosphate antiporter activity / Gluconeogenesis / phosphate ion transmembrane transport / gluconeogenesis / glucose metabolic process / glucose homeostasis / endoplasmic reticulum membrane / endoplasmic reticulum / membrane
Similarity search - Function
Glycerate/sugar phosphate transporter, conserved site / : / glpT family of transporters signature. / Sugar phosphate transporter / Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
Glucose-6-phosphate exchanger SLC37A4
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsZhao Y / Chen Q
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Sci Adv / Year: 2026
Title: Structural insight into the glucose-6-phosphate transport by G6PT1 and inhibition mechanism of CGA.
Authors: Qihao Chen / Pu Yuan / Renjie Li / Xiaoyue Du / Rilei Yu / Yan Zhao /
Abstract: Human glucose-6-phosphate transporter 1 (G6PT1) is responsible for transporting glucose-6-phosphate (G6P) into the endoplasmic reticulum (ER), a crucial rate-limiting step in both glycogenolysis and ...Human glucose-6-phosphate transporter 1 (G6PT1) is responsible for transporting glucose-6-phosphate (G6P) into the endoplasmic reticulum (ER), a crucial rate-limiting step in both glycogenolysis and gluconeogenesis. Complete and chronic dysfunction of G6PT1 can lead to the severe metabolic disorder GSD1b, whereas moderate and reversible inhibition contributes to diabetes treatment. We determined the structures of human G6PT1 in its apo state and in complex with the substrate G6P, cosubstrate phosphate, and the inhibitor chlorogenic acid (CGA). Captured in both lumen- and cytosol-facing conformations, these structures reveal the specific mechanism of phosphate-coupled G6P transport. In addition, the CGA-bound G6PT1 complex shows that CGA stabilizes the transporter in the cytosol-facing conformation, inhibiting it by competing with substrate binding and preventing conformational transitions, providing previously unreported insights into G6PT1 inhibition. Our findings provide a structural foundation for understanding the mechanisms of substrate recognition, transport, drug inhibition, and the pharmacology of G6PT1, paving the way to the rational design of potential therapeutic agents.
History
DepositionJan 21, 2025-
Header (metadata) releaseDec 31, 2025-
Map releaseDec 31, 2025-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_63231.png

Downloads & links

-
Map

FileDownload / File: emd_63231.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.232
Minimum - Maximum-1.119422 - 1.5424242
Average (Standard dev.)0.000090486144 (±0.031372637)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 272.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_63231_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_63231_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Cryo-EM structure of lumen facing G6PT1 in the apo state

EntireName: Cryo-EM structure of lumen facing G6PT1 in the apo state
Components
  • Complex: Cryo-EM structure of lumen facing G6PT1 in the apo state
    • Protein or peptide: Glucose-6-phosphate exchanger SLC37A4
  • Ligand: Lauryl Maltose Neopentyl Glycol

-
Supramolecule #1: Cryo-EM structure of lumen facing G6PT1 in the apo state

SupramoleculeName: Cryo-EM structure of lumen facing G6PT1 in the apo state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Glucose-6-phosphate exchanger SLC37A4

MacromoleculeName: Glucose-6-phosphate exchanger SLC37A4 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.391809 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAAQGYGYYR TVIFSAMFGG YSLYYFNRKT FSFVMPSLVE EIPLDKDDLG FITSSQSAAY AISKFVSGVL SDQMSARWLF SSGLLLVGL VNIFFAWSST VPVFAALWFL NGLAQGLGWP PCGKVLRKWF EPSQFGTWWA ILSTSMNLAG GLGPILATIL A QSYSWRST ...String:
MAAQGYGYYR TVIFSAMFGG YSLYYFNRKT FSFVMPSLVE EIPLDKDDLG FITSSQSAAY AISKFVSGVL SDQMSARWLF SSGLLLVGL VNIFFAWSST VPVFAALWFL NGLAQGLGWP PCGKVLRKWF EPSQFGTWWA ILSTSMNLAG GLGPILATIL A QSYSWRST LALSGALCVV VSFLCLLLIH NEPADVGLRN LDPMPSEGKK GSLKEESTLQ ELLLSPYLWV LSTGYLVVFG VK TCCTDWG QFFLIQEKGQ SALVGSSYMS ALEVGGLVGS IAAGYLSDRA MAKAGLSNYG NPRHGLLLFM MAGMTVSMYL FRV TVTSDS PKLWILVLGA VFGFSSYGPI ALFGVIANES APPNLCGTSH AIVGLMANVG GFLAGLPFST IAKHYSWSTA FWVA EVICA ASTAAFFLLR NIRTKMGRVS KKAE

UniProtKB: Glucose-6-phosphate exchanger SLC37A4

-
Macromolecule #2: Lauryl Maltose Neopentyl Glycol

MacromoleculeName: Lauryl Maltose Neopentyl Glycol / type: ligand / ID: 2 / Number of copies: 4 / Formula: LMN
Molecular weightTheoretical: 1.005188 KDa
Chemical component information

ChemComp-AV0:
Lauryl Maltose Neopentyl Glycol

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 80454
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