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- EMDB-61814: Human glucose 6 phosphate catalytic subunit 1 (hG6PC1) bound with F6P. -

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Basic information

Entry
Database: EMDB / ID: EMD-61814
TitleHuman glucose 6 phosphate catalytic subunit 1 (hG6PC1) bound with F6P.
Map data
Sample
  • Complex: Glucose 6 phosphate catalytic subunit 1
    • Protein or peptide: Glucose-6-phosphatase catalytic subunit 1,GSlinker-HRV3C-GFP-twin strep
  • Ligand: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
  • Ligand: 6-O-phosphono-beta-D-fructofuranose
Keywordsmembrane protein / glucose metabolism / HYDROLASE
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: 3.3 Å
AuthorsChen Q / Zhao Y / Wang Y
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Cell Discov / Year: 2025
Title: The induced-fit and catalytic mechanisms of human G6PC1.
Authors: Qihao Chen / Yuhang Wang / Renjie Li / Qinru Bai / Yan Zhao /
Abstract: Human glucose-6-phosphatase catalytic subunit 1 (hG6PC1) is a key enzyme in glucose metabolism, governing the final common step of gluconeogenesis and glycogenolysis, and directly regulating energy ...Human glucose-6-phosphatase catalytic subunit 1 (hG6PC1) is a key enzyme in glucose metabolism, governing the final common step of gluconeogenesis and glycogenolysis, and directly regulating energy homeostasis. Aberrant mutations in G6PC1 directly cause glycogen storage disease type 1a, which is characterized by chronic hypoglycemia and glycogen accumulation. Additionally, abnormal G6PC1 function leads to increased fasting blood glucose. Consequently, it is a critical target for treating glucose metabolism disorders. In this study, we determine the cryo-EM structures of G6PC1 in both the partially open and fully open states, in either the apo form or in complex with the substrates G6P or F6P and the product phosphate. These structures offer distinct insights into the mechanism of hydrolysis and induced-fit, providing a structural foundation for the diagnostic analysis of disease-causing mutations in G6PC1. Moreover, we propose a potential mechanism by which phosphatidylserine regulates G6PC1 activity, providing a novel perspective on its role and implications.
History
DepositionOct 5, 2024-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateAug 6, 2025-
Current statusAug 6, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61814.png

Downloads & links

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Map

FileDownload / File: emd_61814.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 256 pix.
= 217.6 Å		0.85 Å/pix.
x 256 pix.
= 217.6 Å		0.85 Å/pix.
x 256 pix.
= 217.6 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.223
Minimum - Maximum-1.6562701 - 2.1147065
Average (Standard dev.)0.00029177952 (±0.046128776)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 217.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61814_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61814_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Glucose 6 phosphate catalytic subunit 1

EntireName: Glucose 6 phosphate catalytic subunit 1
Components
  • Complex: Glucose 6 phosphate catalytic subunit 1
    • Protein or peptide: Glucose-6-phosphatase catalytic subunit 1,GSlinker-HRV3C-GFP-twin strep
  • Ligand: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
  • Ligand: 6-O-phosphono-beta-D-fructofuranose

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Supramolecule #1: Glucose 6 phosphate catalytic subunit 1

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

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Macromolecule #1: Glucose-6-phosphatase catalytic subunit 1,GSlinker-HRV3C-GFP-twin...

MacromoleculeName: Glucose-6-phosphatase catalytic subunit 1,GSlinker-HRV3C-GFP-twin strep
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: 71.877039 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 SRIYLAANFP HQVVAGVLSG IAVAETFSHI HSIYNASLKK YFLITFFLFS FAIGFYLLLK GLGVDLLWTL EK AQRWCEQ PEWVHIDTTP FASLLKNLGT LFGLGLALNS SMYRESCKGK LSKWLPFRLS SIVASLVLLH VFDSLKPPSQ VEL VFYVLS FCKSAVVPLA SVSVIPYCLA QVLGQPHKKS LGGSGGGSGG GSGGGSGGGA AALEVLFQGP SKGEELFTGV VPIL VELDG DVNGHKFSVR GEGEGDATNG KLTLKFICTT GKLPVPWPTL VTTLTYGVQC FSRYPDHMKR HDFFKSAMPE GYVQE RTIS FKDDGTYKTR AEVKFEGDTL VNRIELKGID FKEDGNILGH KLEYNFNSHN VYITADKQKN GIKANFKIRH NVEDGS VQL ADHYQQNTPI GDGPVLLPDN HYLSTQSVLS KDPNEKRDHM VLLEFVTAAG ITHGMDEWSH PQFEKGGGSG GGSGGSA WS HPQFEK

UniProtKB: Glucose-6-phosphatase catalytic subunit 1

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Macromolecule #2: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phospho...

MacromoleculeName: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
type: ligand / ID: 2 / Number of copies: 1 / Formula: P5S
Molecular weightTheoretical: 792.075 Da
Chemical component information

ChemComp-P5S:
O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine

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Macromolecule #3: 6-O-phosphono-beta-D-fructofuranose

MacromoleculeName: 6-O-phosphono-beta-D-fructofuranose / type: ligand / ID: 3 / Number of copies: 1 / Formula: F6P
Molecular weightTheoretical: 260.136 Da
Chemical component information

ChemComp-F6P:
6-O-phosphono-beta-D-fructofuranose

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (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: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 55196
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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