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- PDB-9kmn: Structure of hSGLT2-MAP17 complex in the substrate-bound inward-f... -

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Basic information

Entry
Database: PDB / ID: 9kmn
TitleStructure of hSGLT2-MAP17 complex in the substrate-bound inward-facing conformation
Components
  • PDZK1-interacting protein 1
  • Sodium/glucose cotransporter 2
  • mFab90-H
  • mFab90-L
KeywordsTRANSPORT PROTEIN / glucose transporter / SGLT / sodium glucose transporter / membrane 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.47 Å
AuthorsChen, L. / Cui, W. / Sun, Z.
Funding support China, 2items
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, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Additional map / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Mask / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2025Group: Data collection / Structure summary / Category: chem_comp / em_admin / Item: _chem_comp.pdbx_synonyms / _em_admin.last_update
Revision 1.1Oct 15, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Experimental summary / Structure summary / Data content type: EM metadata / Category: em_admin / Data content type: EM metadata / EM metadata / Item: _chem_comp.pdbx_synonyms / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sodium/glucose cotransporter 2
B: PDZK1-interacting protein 1
H: mFab90-H
L: mFab90-L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,4235
Polymers104,2414
Non-polymers1821
Water543
1


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

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Components

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Protein , 4 types, 4 molecules ABHL

#1: Protein Sodium/glucose cotransporter 2 / Na(+)/glucose cotransporter 2 / Low affinity sodium-glucose cotransporter / Solute carrier family 5 member 2


Mass: 72949.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC5A2, SGLT2 / Production host: Homo sapiens (human) / References: UniProt: P31639
#2: Protein PDZK1-interacting protein 1 / 17 kDa membrane-associated protein / Protein DD96


Mass: 12265.092 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDZK1IP1, MAP17 / Production host: Homo sapiens (human) / References: UniProt: Q13113
#3: Protein mFab90-H


Mass: 9975.288 Da / Num. of mol.: 1
Fragment: Author stated: The antibody was developed using hybridoma technique and no molecular biology process was involved. Therefore, neither we nor the company know the sequences of Fab.
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#4: Protein mFab90-L


Mass: 9051.144 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)

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Sugars / Non-polymers , 2 types, 4 molecules

#5: Sugar ChemComp-A1EFW / (2~{S},3~{R},4~{R},5~{S},6~{R})-5-fluoranyl-6-(hydroxymethyl)oxane-2,3,4-triol


Type: D-saccharide, alpha linking / Mass: 182.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11FO5 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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Details

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: human SGLT2-MAP17-mFab90 complex / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
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: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 2.47 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 376800 / Symmetry type: POINT

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