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- EMDB-62439: Structure of hSGLT2-MAP17 complex in the substrate-bound inward-f... -

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Basic information

Entry
Database: EMDB / ID: EMD-62439
TitleStructure of hSGLT2-MAP17 complex in the substrate-bound inward-facing conformation
Map data
Sample
  • Complex: human SGLT2-MAP17-mFab90 complex
    • Protein or peptide: Sodium/glucose cotransporter 2
    • Protein or peptide: PDZK1-interacting protein 1
    • Protein or peptide: mFab90-H
    • Protein or peptide: mFab90-L
  • Ligand: (2~{S},3~{R},4~{R},5~{S},6~{R})-5-fluoranyl-6-(hydroxymethyl)oxane-2,3,4-triol
  • Ligand: water
Keywordsglucose transporter / SGLT / sodium glucose transporter / membrane protein / TRANSPORT PROTEIN
Function / homology
Function and homology information


low-affinity D-glucose:sodium symporter activity / Defective SLC5A2 causes renal glucosuria (GLYS1) / alpha-glucoside transport / alpha-glucoside transmembrane transporter activity / D-glucose:sodium symporter activity / renal D-glucose absorption / hexose transmembrane transport / D-glucose import across plasma membrane / Cellular hexose transport / D-glucose transmembrane transporter activity ...low-affinity D-glucose:sodium symporter activity / Defective SLC5A2 causes renal glucosuria (GLYS1) / alpha-glucoside transport / alpha-glucoside transmembrane transporter activity / D-glucose:sodium symporter activity / renal D-glucose absorption / hexose transmembrane transport / D-glucose import across plasma membrane / Cellular hexose transport / D-glucose transmembrane transporter activity / sodium ion import across plasma membrane / sodium ion transport / carbohydrate metabolic process / apical plasma membrane / extracellular exosome / metal ion binding / membrane / plasma membrane
Similarity search - Function
PDZK1-interacting protein 1/SMIM24 / Membrane-associated protein 117 kDa, PDZK1-interacting protein 1 / Sodium:solute symporter family signature 2. / Sodium:solute symporter family signature 1. / Sodium/solute symporter, conserved site / Sodium/solute symporter / Sodium/glucose symporter superfamily / Sodium:solute symporter family / Sodium:solute symporter family profile.
Similarity search - Domain/homology
Sodium/glucose cotransporter 2 / PDZK1-interacting protein 1
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.47 Å
AuthorsChen L / Cui W / Sun Z
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)3240050 China
National Natural Science Foundation of China (NSFC)32225027 China
CitationJournal: Nat Commun / Year: 2025
Title: Mechanism of substrate recognition and release of human SGLT2.
Authors: Wenhao Cui / Zejian Sun / Jiaxuan Xu / Xiaoyu Liu / Yunlu Kang / Lei Chen /
Abstract: Glucose is a vital energy source essential for life and human health. Sodium-glucose cotransporter 2 (SGLT2) is a sodium-glucose symporter that utilizes the electrochemical gradient of sodium to ...Glucose is a vital energy source essential for life and human health. Sodium-glucose cotransporter 2 (SGLT2) is a sodium-glucose symporter that utilizes the electrochemical gradient of sodium to reabsorb glucose from kidney filtrate back into circulation. SGLT2 plays a crucial role in maintaining blood glucose homeostasis and is an important drug target for type 2 diabetes. Despite its significance, the mechanisms by which SGLT2 recognizes and releases substrates during its transport cycle remain largely unknown. Here, we present structures of human SGLT2 in complex with a glucose analogue in the occluded conformation at 2.6 Å resolution, revealing a detailed hydrogen bonding network at the substrate binding site that governs substrate recognition. Additionally, structures of SGLT2 in both the substrate-bound inward-facing conformation and the substrate-free inward-facing conformations illustrate the structural changes that occur during substrate release into cytosol. Our structural analysis, combined with mutagenesis results, identifies specific polar interactions that are essential for maintaining the outer and inner gates in their closed conformations.
History
DepositionNov 16, 2024-
Header (metadata) releaseSep 3, 2025-
Map releaseSep 3, 2025-
UpdateSep 3, 2025-
Current statusSep 3, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62439.png

Downloads & links

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Map

FileDownload / File: emd_62439.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 280 pix.
= 266.88 Å		0.95 Å/pix.
x 280 pix.
= 266.88 Å		0.95 Å/pix.
x 280 pix.
= 266.88 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95314 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.905
Minimum - Maximum-6.478025 - 8.980047000000001
Average (Standard dev.)0.00032429412 (±0.18547323)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 266.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_62439_msk_1.map
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Additional map: #1

Fileemd_62439_additional_1.map
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Half map: #2

Fileemd_62439_half_map_1.map
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Half map: #1

Fileemd_62439_half_map_2.map
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Sample components

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Entire : human SGLT2-MAP17-mFab90 complex

EntireName: human SGLT2-MAP17-mFab90 complex
Components
  • Complex: human SGLT2-MAP17-mFab90 complex
    • Protein or peptide: Sodium/glucose cotransporter 2
    • Protein or peptide: PDZK1-interacting protein 1
    • Protein or peptide: mFab90-H
    • Protein or peptide: mFab90-L
  • Ligand: (2~{S},3~{R},4~{R},5~{S},6~{R})-5-fluoranyl-6-(hydroxymethyl)oxane-2,3,4-triol
  • Ligand: water

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Supramolecule #1: human SGLT2-MAP17-mFab90 complex

SupramoleculeName: human SGLT2-MAP17-mFab90 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Sodium/glucose cotransporter 2

MacromoleculeName: Sodium/glucose cotransporter 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 72.949414 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEEHTEAGSA PEMGAQKALI DNPADILVIA AYFLLVIGVG LWSMCRTNRG TVGGYFLAGR SMVWWPVGAS LFASNIGSGH FVGLAGTGA ASGLAVAGFE WNALFVVLLL GWLFAPVYLT AGVITMPQYL RKRFGGRRIR LYLSVLSLFL YIFTKISVDM F SGAVFIQQ ...String:
MEEHTEAGSA PEMGAQKALI DNPADILVIA AYFLLVIGVG LWSMCRTNRG TVGGYFLAGR SMVWWPVGAS LFASNIGSGH FVGLAGTGA ASGLAVAGFE WNALFVVLLL GWLFAPVYLT AGVITMPQYL RKRFGGRRIR LYLSVLSLFL YIFTKISVDM F SGAVFIQQ ALGWNIYASV IALLGITMIY TVTGGLAALM YTDTVQTFVI LGGACILMGY AFHEVGGYSG LFDKYLGAAT SL TVSEDPA VGNISSFCYR PRPDSYHLLR HPVTGDLPWP ALLLGLTIVS GWYWCSDQVI VQRCLAGKSL THIKAGCILC GYL KLTPMF LMVMPGMISR ILYPDEVACV VPEVCRRVCG TEVGCSNIAY PRLVVKLMPN GLRGLMLAVM LAALMSSLAS IFNS SSTLF TMDIYTRLRP RAGDRELLLV GRLWVVFIVV VSVAWLPVVQ AAQGGQLFDY IQAVSSYLAP PVSAVFVLAL FVPRV NEQG AFWGLIGGLL MGLARLIPEF SFGSGSCVQP SACPAFLCGV HYLYFAIVLF FCSGLLTLTV SLCTAPIPRK HLHRLV FSL RHSKEEREDL DADEQQGSSL PVQNGCPESA MEMNEPQAPA PSLFRQCLLW FCGMSRGGVG SPPPLTQEEA AAAARRL ED ISEDPSWARV VNLNALLMMA VAVFLWGFYA

UniProtKB: Sodium/glucose cotransporter 2

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Macromolecule #2: PDZK1-interacting protein 1

MacromoleculeName: PDZK1-interacting protein 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.265092 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MSALSLLILG LLMAVPPASC QQGLGNLQPW MQGLIAVAVF LVLVAIAFAV NHFWCQEEPE PAHMILTVGN KADGVLVGTD GRYSSMAAS FRSSEHENAY ENVPEEEGKV RSTPM

UniProtKB: PDZK1-interacting protein 1

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Macromolecule #3: mFab90-H

MacromoleculeName: mFab90-H / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 9.975288 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)

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Macromolecule #4: mFab90-L

MacromoleculeName: mFab90-L / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 9.051144 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)P (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)

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Macromolecule #5: (2~{S},3~{R},4~{R},5~{S},6~{R})-5-fluoranyl-6-(hydroxymethyl)oxan...

MacromoleculeName: (2~{S},3~{R},4~{R},5~{S},6~{R})-5-fluoranyl-6-(hydroxymethyl)oxane-2,3,4-triol
type: ligand / ID: 5 / Number of copies: 1 / Formula: A1EFW
Molecular weightTheoretical: 182.147 Da

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 3 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.47 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 376800
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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