[English] 日本語
Yorodumi
- EMDB-66728: cryoEM structure of G6PT monomer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-66728
TitlecryoEM structure of G6PT monomer
Map data
Sample
  • Complex: Glucose-6-phosphate translocase
    • Protein or peptide: Glucose-6-phosphate exchanger SLC37A4
KeywordsGlucose-6-Phosphate Translocase / G6PT / SLC37A4 / 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: 3.08 Å
AuthorsZhang WQ / Jiao HZ / Hu HL / Guo X
Funding support1 items
OrganizationGrant numberCountry
Other government
CitationJournal: PLoS Biol / Year: 2026
Title: Structures of the human glucose-6-phosphate transporter provide insights into its transport cycle and substrate recognition.
Authors: Wanqin Zhang / Haizhan Jiao / Jingchuan Xue / Jiao Zhou / Yuye Wang / Qi Pan / Yuting Guo / Geshu Zhang / Hongli Hu / Xue Guo /
Abstract: The human glucose-6-phosphate transporter (G6PT/SLC37A4) mediates the translocation of glucose-6-phosphate (G6P) from the cytoplasm into the endoplasmic reticulum, a process essential for glucose ...The human glucose-6-phosphate transporter (G6PT/SLC37A4) mediates the translocation of glucose-6-phosphate (G6P) from the cytoplasm into the endoplasmic reticulum, a process essential for glucose production and the maintenance of blood glucose homeostasis between meals. Dysfunction of G6PT causes glycogen storage disease type Ib (GSD-Ib), a severe metabolic disorder characterized by hypoglycemia, hepatomegaly, and neutropenia. Despite its physiological and clinical significance, the structural basis of G6P recognition and the molecular mechanisms underlying GSD-Ib have remained elusive. Here, we present cryo-electron microscopy structures of human G6PT, revealing a monomer in an outward-open state at 3.1 Å and a homodimeric assembly in a face-to-face topology at 3.3 Å. By combining computational modeling of the G6P-G6PT complexes with functional characterization, we have uncovered the key molecular elements that govern the alternating-access mechanism: an electropositive substrate-binding pocket tailored for phosphorylated sugars; conserved aromatic residues that seal the cytosolic gate; and a dynamic inter-domain salt bridge that regulates the conformational transition. Our work provides fundamental insights into the transport cycle of the organophosphate:phosphate antiporter (OPA) family, offers a framework for interpreting GSD-Ib pathology at the molecular level, and establishes a foundation for advancing the mechanistic understanding of the human SLC37 family.
History
DepositionOct 25, 2025-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_66728.png

Downloads & links

-
Map

FileDownload / File: emd_66728.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: 0.01
Minimum - Maximum-0.041812718 - 0.06031743
Average (Standard dev.)-0.000019381052 (±0.001147673)
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

-
Additional map: #1

Fileemd_66728_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_66728_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_66728_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Glucose-6-phosphate translocase

EntireName: Glucose-6-phosphate translocase
Components
  • Complex: Glucose-6-phosphate translocase
    • Protein or peptide: Glucose-6-phosphate exchanger SLC37A4

-
Supramolecule #1: Glucose-6-phosphate translocase

SupramoleculeName: Glucose-6-phosphate translocase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.025609 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKA SRATMAAQGY GYYRTVIFSA MFGGYSLYYF NRKTFSFVMP SLVEEIPLDK DDLGFITSSQ SAAYAISKFV SGVLSDQMS ARWLFSSGLL LVGLVNIFFA WSSTVPVFAA LWFLNGLAQG LGWPPCGKVL RKWFEPSQFG TWWAILSTSM N LAGGLGPI ...String:
MDYKDDDDKA SRATMAAQGY GYYRTVIFSA MFGGYSLYYF NRKTFSFVMP SLVEEIPLDK DDLGFITSSQ SAAYAISKFV SGVLSDQMS ARWLFSSGLL LVGLVNIFFA WSSTVPVFAA LWFLNGLAQG LGWPPCGKVL RKWFEPSQFG TWWAILSTSM N LAGGLGPI LATILAQSYS WRSTLALSGA LCVVVSFLCL LLIHNEPADV GLRNLDPMPS EGKKGSLKEE STLQELLLSP YL WVLSTGY LVVFGVKTCC TDWGQFFLIQ EKGQSALVGS SYMSALEVGG LVGSIAAGYL SDRAMAKAGL SNYGNPRHGL LLF MMAGMT VSMYLFRVTV TSDSPKLWIL VLGAVFGFSS YGPIALFGVI ANESAPPNLC GTSHAIVGLM ANVGGFLAGL PFST IAKHY SWSTAFWVAE VICAASTAAF FLLRNIRTKM GRVSKKAESN SLEVLFQ

UniProtKB: Glucose-6-phosphate exchanger SLC37A4

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 51.38 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 92736
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: PROJECTION MATCHING
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