[English] 日本語
Yorodumi
- EMDB-61210: H176A mutant of human G6PC1 in complex with G6P -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-61210
TitleH176A mutant of human G6PC1 in complex with G6P
Map data
Sample
  • Complex: Glucose-6-phosphatase catalytic subunit1
    • Protein or peptide: Glucose-6-phosphatase catalytic subunit 1
  • Ligand: 6-O-phosphono-beta-D-glucopyranose
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
KeywordsG6PC1 / cryo-EM / G6P / STRUCTURAL PROTEIN
Function / homology
Function and homology information


glucose-6-phosphatase / Glycogen storage disease type Ia (G6PC) / glucose-6-phosphate transport / glucose-6-phosphatase activity / phosphotransferase activity, alcohol group as acceptor / response to resveratrol / urate metabolic process / glucose 6-phosphate metabolic process / Gluconeogenesis / response to carbohydrate ...glucose-6-phosphatase / Glycogen storage disease type Ia (G6PC) / glucose-6-phosphate transport / glucose-6-phosphatase activity / phosphotransferase activity, alcohol group as acceptor / response to resveratrol / urate metabolic process / glucose 6-phosphate metabolic process / Gluconeogenesis / response to carbohydrate / glycogen catabolic process / triglyceride metabolic process / response to food / glycogen metabolic process / phosphate ion binding / steroid metabolic process / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / cholesterol homeostasis / gluconeogenesis / multicellular organism growth / cellular response to insulin stimulus / glucose homeostasis / regulation of gene expression / endoplasmic reticulum membrane / membrane
Similarity search - Function
Glucose-6-phosphatase / Acid phosphatase homologues / Phosphatidic acid phosphatase type 2/haloperoxidase / PAP2 superfamily / Phosphatidic acid phosphatase type 2/haloperoxidase superfamily
Similarity search - Domain/homology
Glucose-6-phosphatase catalytic subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.14 Å
AuthorsJiang DH / Xia ZY
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971134 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Structural insights into glucose-6-phosphate recognition and hydrolysis by human G6PC1.
Authors: Zhanyi Xia / Chuanyu Liu / Di Wu / Huiwen Chen / Jun Zhao / Daohua Jiang /
Abstract: The glucose-6-phosphatase (G6Pase) is an integral membrane protein that catalyzes the hydrolysis of glucose-6-phosphate (G6P) in the endoplasmic reticulum lumen and plays a vital role in glucose ...The glucose-6-phosphatase (G6Pase) is an integral membrane protein that catalyzes the hydrolysis of glucose-6-phosphate (G6P) in the endoplasmic reticulum lumen and plays a vital role in glucose homeostasis. Dysregulation or genetic mutations of G6Pase are associated with diabetes and glycogen storage disease 1a (GSD-1a). Studies have characterized the biophysical and biochemical properties of G6Pase; however, the structure and substrate recognition mechanism of G6Pase remain unclear. Here, we present two cryo-EM structures of the 40-kDa human G6Pase: a wild-type apo form and a mutant G6Pase-H176A with G6P bound, elucidating the structural basis for substrate recognition and hydrolysis. G6Pase comprises nine transmembrane helices and possesses a large catalytic pocket facing the lumen. Unexpectedly, G6P binding induces substantial conformational rearrangements in the catalytic pocket, which facilitate the binding of the sugar moiety. In conjunction with functional analyses, this study provides critical insights into the structure, substrate recognition, catalytic mechanism, and pathology of G6Pase.
History
DepositionAug 19, 2024-
Header (metadata) releaseFeb 5, 2025-
Map releaseFeb 5, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_61210.png

Downloads & links

-
Map

FileDownload / File: emd_61210.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: 0.355
Minimum - Maximum-1.5755587 - 2.267247
Average (Standard dev.)-0.00046766884 (±0.033789728)
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_61210_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_61210_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Glucose-6-phosphatase catalytic subunit1

EntireName: Glucose-6-phosphatase catalytic subunit1
Components
  • Complex: Glucose-6-phosphatase catalytic subunit1
    • Protein or peptide: Glucose-6-phosphatase catalytic subunit 1
  • Ligand: 6-O-phosphono-beta-D-glucopyranose
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate

-
Supramolecule #1: Glucose-6-phosphatase catalytic subunit1

SupramoleculeName: Glucose-6-phosphatase catalytic subunit1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Glucose-6-phosphatase catalytic subunit 1

MacromoleculeName: Glucose-6-phosphatase catalytic subunit 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: glucose-6-phosphatase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.855504 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEEGMNVLHD FGIQSTHYLQ VNYQDSQDWF ILVSVIADLR NAFYVLFPIW FHLQEAVGIK LLWVAVIGDW LNLVFKWILF GQRPYWWVL DTDYYSNTSV PLIKQFPVTC ETGPGSPSGH AMGTAGVYYV MVTSTLSIFQ GKIKPTYRFR CLNVILWLGF W AVQLNVCL ...String:
MEEGMNVLHD FGIQSTHYLQ VNYQDSQDWF ILVSVIADLR NAFYVLFPIW FHLQEAVGIK LLWVAVIGDW LNLVFKWILF GQRPYWWVL DTDYYSNTSV PLIKQFPVTC ETGPGSPSGH AMGTAGVYYV MVTSTLSIFQ GKIKPTYRFR CLNVILWLGF W AVQLNVCL SRIYLAAAFP HQVVAGVLSG IAVAETFSHI HSIYNASLKK YFLITFFLFS FAIGFYLLLK GLGVDLLWTL EK AQRWCEQ PEWVHIDTTP FASLLKNLGT LFGLGLALNS SMYRESCKGK LSKWLPFRLS SIVASLVLLH VFDSLKPPSQ VEL VFYVLS FCKSAVVPLA SVSVIPYCLA QVLGQP

UniProtKB: Glucose-6-phosphatase catalytic subunit 1

-
Macromolecule #2: 6-O-phosphono-beta-D-glucopyranose

MacromoleculeName: 6-O-phosphono-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 1 / Formula: BG6
Molecular weightTheoretical: 260.136 Da
Chemical component information

ChemComp-BG6:
6-O-phosphono-beta-D-glucopyranose

-
Macromolecule #3: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...

MacromoleculeName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
type: ligand / ID: 3 / Number of copies: 3 / Formula: POV
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
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: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 170633
Initial angle assignmentType: RANDOM ASSIGNMENT
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