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- EMDB-63190: Cryo-EM structure of G6PT1 in complex with Glucose-6-phosphate -

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Basic information

Entry
Database: EMDB / ID: EMD-63190
TitleCryo-EM structure of G6PT1 in complex with Glucose-6-phosphate
Map data
Sample
  • Complex: Cryo-EM structure of G6PT1 in complex with Glucose-6-phosphate
    • Protein or peptide: Glucose-6-phosphate exchanger SLC37A4
  • Ligand: 6-O-phosphono-beta-D-glucopyranose
Keywordsprotein structure / STRUCTURAL PROTEIN / TRANSPORT PROTEIN
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
Glucose-6-phosphate exchanger SLC37A4
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsZhao Y / Chen Q
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Transport and inhibition mechanisms of G6PT1
Authors: Zhao Y / Chen Q
History
DepositionJan 17, 2025-
Header (metadata) releaseDec 31, 2025-
Map releaseDec 31, 2025-
UpdateDec 31, 2025-
Current statusDec 31, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63190.png

Downloads & links

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Map

FileDownload / File: emd_63190.map.gz / Format: CCP4 / Size: 64 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 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

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: 0.256
Minimum - Maximum-1.7704439 - 2.3072934
Average (Standard dev.)0.000026361678 (±0.04671822)
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_63190_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_63190_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of G6PT1 in complex with Glucose-6-phosphate

EntireName: Cryo-EM structure of G6PT1 in complex with Glucose-6-phosphate
Components
  • Complex: Cryo-EM structure of G6PT1 in complex with Glucose-6-phosphate
    • Protein or peptide: Glucose-6-phosphate exchanger SLC37A4
  • Ligand: 6-O-phosphono-beta-D-glucopyranose

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Supramolecule #1: Cryo-EM structure of G6PT1 in complex with Glucose-6-phosphate

SupramoleculeName: Cryo-EM structure of G6PT1 in complex with Glucose-6-phosphate
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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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: 45.444695 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GYGYYRTVIF SAMFGGYSLY YFNRKTFSFV MPSLVEEIPL DKDDLGFITS SQSAAYAISK FVSGVLSDQM SARWLFSSGL LLVGLVNIF FAWSSTVPVF AALWFLNGLA QGLGWPPCGK VLRKWFEPSQ FGTWWAILST SMNLAGGLGP ILATILAQSY S WRSTLALS ...String:
GYGYYRTVIF SAMFGGYSLY YFNRKTFSFV MPSLVEEIPL DKDDLGFITS SQSAAYAISK FVSGVLSDQM SARWLFSSGL LLVGLVNIF FAWSSTVPVF AALWFLNGLA QGLGWPPCGK VLRKWFEPSQ FGTWWAILST SMNLAGGLGP ILATILAQSY S WRSTLALS GALCVVVSFL CLLLIHNEPA DVGLRNLDPM PSEGKKGSLK EESTLQELLL SPYLWVLSTG YLVVFGVKTC CT DWGQFFL IQEKGQSALV GSSYMSALEV GGLVGSIAAG YLSDRAMAKA GLSNYGNPRH GLLLFMMAGM TVSMYLFRVT VTS DSPKLW ILVLGAVFGF SSYGPIALFG VIANESAPPN LCGTSHAIVG LMANVGGFLA GLPFSTIAKH YSWSTAFWVA EVIC AASTA AFFLLRNIRT KMGRV

UniProtKB: Glucose-6-phosphate exchanger SLC37A4

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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

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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 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 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: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 58851
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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