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- EMDB-65554: Human SLC37A4 lateral dimer -

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Basic information

Entry
Database: EMDB / ID: EMD-65554
TitleHuman SLC37A4 lateral dimer
Map data
Sample
  • Complex: Human SLC37A4
    • Protein or peptide: Glucose-6-phosphate exchanger SLC37A4,Soluble cytochrome b562
KeywordsSLC37A4 / G6PT / G6P / GSD-Ib / 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 / electron transport chain / glucose metabolic process / glucose homeostasis ...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 / electron transport chain / glucose metabolic process / glucose homeostasis / periplasmic space / electron transfer activity / iron ion binding / heme binding / 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. / Cytochrome b562 / Cytochrome b562 ...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. / Cytochrome b562 / Cytochrome b562 / MFS transporter superfamily / Cytochrome c/b562
Similarity search - Domain/homology
Glucose-6-phosphate exchanger SLC37A4 / Soluble cytochrome b562
Similarity search - Component
Biological speciesHomo sapiens (human) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsZhou D / Zhang Z
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32471252 China
Ministry of Science and Technology (MoST, China)2021YFA1302300 China
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Structural basis of G6P/Pi transport and inhibition in SLC37A4.
Authors: Dong Zhou / Yang Zhang / Nanhao Chen / Shitang Huang / Chen Song / Zhe Zhang /
Abstract: Glycogen storage disease type Ib (GSD-Ib), caused by loss-of-function mutations in the endoplasmic reticulum transporter SLC37A4, disrupts glucose homeostasis through impaired glucose-6-phosphate ...Glycogen storage disease type Ib (GSD-Ib), caused by loss-of-function mutations in the endoplasmic reticulum transporter SLC37A4, disrupts glucose homeostasis through impaired glucose-6-phosphate (G6P)/phosphate (Pi) antiport. Despite its central role in glycogen metabolism and immune regulation, the structural mechanisms governing SLC37A4's transport cycle and pathological dysfunction remain elusive. Here we report cryo-electron microscopy structures of human SLC37A4 in four functional states, capturing conformational transitions between lumen-facing and cytoplasm-facing states. Combined with mutational analysis, molecular dynamics simulations and functional assays, we identify a conserved substrate-binding pocket that alternately accommodates G6P and Pi through electrostatic complementarity and domain-dependent interactions. We further demonstrate that the high-affinity inhibitor S-4048 sterically occludes the cytoplasmic entry pathway by trapping the transporter in a cytoplasm-facing conformation. Our work elucidates the molecular pathology of GSD-Ib-linked mutations and provides a structural framework for developing therapies targeting this transporter in metabolic diseases.
History
DepositionJul 26, 2025-
Header (metadata) releaseNov 19, 2025-
Map releaseNov 19, 2025-
UpdateNov 26, 2025-
Current statusNov 26, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65554.png

Downloads & links

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Map

FileDownload / File: emd_65554.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-1.0113112 - 1.6339451
Average (Standard dev.)0.00021804418 (±0.02995817)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 298.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_65554_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_65554_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 : Human SLC37A4

EntireName: Human SLC37A4
Components
  • Complex: Human SLC37A4
    • Protein or peptide: Glucose-6-phosphate exchanger SLC37A4,Soluble cytochrome b562

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Supramolecule #1: Human SLC37A4

SupramoleculeName: Human SLC37A4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 120 KDa

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Macromolecule #1: Glucose-6-phosphate exchanger SLC37A4,Soluble cytochrome b562

MacromoleculeName: Glucose-6-phosphate exchanger SLC37A4,Soluble cytochrome b562
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 60.194102 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAAQGYGYYR TVIFSAMFGG YSLYYFNRKT FSFVMPSLVE EIPLDKDDLG FITSSQSAAY AISKFVSGVL SDQMSARWLF SSGLLLVGL VNIFFAWSST VPVFAALWFL NGLAQGLGWP PCGKVLRKWF EPSQFGTWWA ILSTSMNLAG GLGPILATIL A QSYSWRST ...String:
MAAQGYGYYR TVIFSAMFGG YSLYYFNRKT FSFVMPSLVE EIPLDKDDLG FITSSQSAAY AISKFVSGVL SDQMSARWLF SSGLLLVGL VNIFFAWSST VPVFAALWFL NGLAQGLGWP PCGKVLRKWF EPSQFGTWWA ILSTSMNLAG GLGPILATIL A QSYSWRST LALSGALCVV VSFLCLLLIH NEPADVGLRN LDPMPSEGKK GSLKEESTLQ ELLLSPYLWV LSTGYLVVFG VK TCCTDWG QFFLIQEKGQ SALVGSSYMS ALEVGGLVGS IAAGYLSDRA MAKAGLSNYG NPRHGLLLFM MAGMTVSMYL FRV TVTSDS PKLWILVLGA VFGFSSYGPI ALFGVIANES APPNLCGTSH AIVGLMANVG GFLAGLPFST IAKHYSWSTA FWVA EVICA ASTAAFFLLR AEEEKRKAEE EKRKAEEEKR KADLEDNWET LNDNLKVIEK ADNAAQVKDA LTKMRAAALD AQKAT PPKL EDKSPDSPEM KDFRHGFDIL VGQIDDALKL ANEGKVKEAQ AAAEQLKTTR NAYIQKYLSN SLEVLFQ

UniProtKB: Glucose-6-phosphate exchanger SLC37A4, Soluble cytochrome b562

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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

Concentration6 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
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: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 86909
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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