[English] 日本語
Yorodumi
- PDB-9x97: Cryo-EM Structure of G6PT1 bound with upper pi -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9x97
TitleCryo-EM Structure of G6PT1 bound with upper pi
ComponentsGlucose-6-phosphate exchanger SLC37A4
KeywordsTRANSPORT PROTEIN / G6P
Function / homology
Function and homology information


glucose-6-phosphate transmembrane transporter activity / Glycogen storage disease type Ib (SLC37A4) / glucose 6-phosphate:phosphate antiporter activity / glucose-6-phosphate transport / 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:phosphate antiporter activity / glucose-6-phosphate transport / 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
PHOSPHATE ION / Glucose-6-phosphate exchanger SLC37A4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.89 Å
AuthorsShuai, G. / Xia, Y. / Qian, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22477098 China
CitationJournal: Nat Commun / Year: 2025
Title: Structures of human glucose-6-phosphate transporter reveal reciprocal antiport mechanism driving glucose-6-phosphate and inorganic phosphate exchange.
Authors: Qian Wang / Ningjie Guo / Yunxiang Du / Junwu Liu / Wanting Ai / Fengyi Yang / Yuanzai Zhu / Yuanyuan Zhao / Di Wu / Lei Liu / Xia Yao / Shuai Gao /
Abstract: Glucose-6-phosphate transporter 1 (G6PT1) is essential for systemic glucose homeostasis, and its deficiency causes glycogen storage disease type 1b (GSD1b). G6PT1 functions as a sugar- ...Glucose-6-phosphate transporter 1 (G6PT1) is essential for systemic glucose homeostasis, and its deficiency causes glycogen storage disease type 1b (GSD1b). G6PT1 functions as a sugar-phosphate/inorganic phosphate (Pi) antiporter, orchestrating G6P transport into the endoplasmic reticulum lumen driven by a Pi gradient. Despite its physiological significance, the molecular mechanisms underlying substrate recognition and antiport activity remain poorly characterized. Here, we present cryo-electron microscopy structures of human G6PT1 in apo, Pi-bound, and GlcN6P-bound (a G6P analogue) states, all captured in cytosol-open conformations. Combined with molecular docking and functional assays, these structures elucidate the molecular basis for Pi and G6P recognition in G6PT1. Comparative analysis reveals that Pi binding triggers an interdomain salt bridge formation, resulting in a thicker luminal gate and a more compact central cavity for G6P binding. In addition to the monomer, we identify a dimeric assembly of G6PT1. Mutating key residues at the dimer interface impairs transport activity, suggesting a regulatory role for oligomerization. Our findings thus provide a mechanistic framework for understanding G6PT1 working mechanism and its pathological dysregulation in GSD1b.
History
DepositionOct 20, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 7, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 7, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 7, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 7, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 7, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 7, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glucose-6-phosphate exchanger SLC37A4
C: Glucose-6-phosphate exchanger SLC37A4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,9744
Polymers92,7842
Non-polymers1902
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein Glucose-6-phosphate exchanger SLC37A4 / Glucose-5-phosphate transporter / Glucose-6-phosphate translocase / Solute carrier family 37 member ...Glucose-5-phosphate transporter / Glucose-6-phosphate translocase / Solute carrier family 37 member 4 / Transformation-related gene 19 protein / TRG-19


Mass: 46391.809 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC37A4, G6PT, G6PT1, PRO0685, TRG19 / Production host: Homo sapiens (human) / References: UniProt: O43826
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: G6PT1 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1900 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30263 / Symmetry type: POINT
RefinementHighest resolution: 2.89 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0076510
ELECTRON MICROSCOPYf_angle_d1.1758858
ELECTRON MICROSCOPYf_dihedral_angle_d5.382880
ELECTRON MICROSCOPYf_chiral_restr0.041998
ELECTRON MICROSCOPYf_plane_restr0.0061084

+
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