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- PDB-9jtl: Human glucose 6 phosphate catalytic subunit 1 (hG6PC1) in apo state. -

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Basic information

Entry
Database: PDB / ID: 9jtl
TitleHuman glucose 6 phosphate catalytic subunit 1 (hG6PC1) in apo state.
ComponentsGlucose-6-phosphatase catalytic subunit 1,GS linker-HRV3C-GFP-twin strep
KeywordsHYDROLASE / membrane protein / glucose metabolism
Function / homology
Function and homology information


glucose-6-phosphatase / Glycogen storage disease type Ia (G6PC) / glucose-6-phosphatase activity / glucose-6-phosphate transport / 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-phosphatase activity / glucose-6-phosphate transport / 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
Chem-P5S / Glucose-6-phosphatase catalytic subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsChen, Q. / Zhao, Y. / Wang, Y.
Funding support China, 1items
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, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucose-6-phosphatase catalytic subunit 1,GS linker-HRV3C-GFP-twin strep
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,6932
Polymers71,9011
Non-polymers7921
Water00
1


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

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Components

#1: Protein Glucose-6-phosphatase catalytic subunit 1,GS linker-HRV3C-GFP-twin strep / Glucose-6-phosphatase / G-6-Pase / G6Pase / Glucose-6-phosphatase alpha / G6Pase-alpha


Mass: 71901.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: hG6PC1-GS linker-HRV3C-GFP-twin strep / Source: (gene. exp.) Homo sapiens (human) / Gene: G6PC1, G6PC, G6PT / Production host: Homo sapiens (human) / References: UniProt: P35575, glucose-6-phosphatase
#2: Chemical ChemComp-P5S / O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine / phosphatidyl serine


Mass: 792.075 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H82NO10P / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Glucose 6 phosphate catalytic subunit 1 / 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

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 28471 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0032866
ELECTRON MICROSCOPYf_angle_d0.5593911
ELECTRON MICROSCOPYf_dihedral_angle_d3.96367
ELECTRON MICROSCOPYf_chiral_restr0.04442
ELECTRON MICROSCOPYf_plane_restr0.005474

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