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- PDB-8hb0: Structure of human SGLT2-MAP17 complex with TA1887 -

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Basic information

Entry
Database: PDB / ID: 8hb0
TitleStructure of human SGLT2-MAP17 complex with TA1887
Components
  • PDZK1-interacting protein 1
  • Sodium/glucose cotransporter 2
KeywordsTRANSPORT PROTEIN / Ion transport / Sodium transport / Sugar transport / Symport
Function / homology
Function and homology information


low-affinity D-glucose:sodium symporter activity / Defective SLC5A2 causes renal glucosuria (GLYS1) / alpha-glucoside transport / D-glucose:sodium symporter activity / alpha-glucoside transmembrane transporter activity / hexose transmembrane transport / D-glucose transmembrane transporter activity / renal D-glucose absorption / Cellular hexose transport / D-glucose import across plasma membrane ...low-affinity D-glucose:sodium symporter activity / Defective SLC5A2 causes renal glucosuria (GLYS1) / alpha-glucoside transport / D-glucose:sodium symporter activity / alpha-glucoside transmembrane transporter activity / hexose transmembrane transport / D-glucose transmembrane transporter activity / renal D-glucose absorption / Cellular hexose transport / D-glucose import across plasma membrane / sodium ion import across plasma membrane / sodium ion transport / carbohydrate metabolic process / apical plasma membrane / extracellular exosome / 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
Chem-KZ3 / Sodium/glucose cotransporter 2 / PDZK1-interacting protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsHiraizumi, M. / Kishida, H. / Miyaguchi, I. / Nureki, O.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Transport and inhibition mechanism of the human SGLT2-MAP17 glucose transporter.
Authors: Masahiro Hiraizumi / Tomoya Akashi / Kouta Murasaki / Hiroyuki Kishida / Taichi Kumanomidou / Nao Torimoto / Osamu Nureki / Ikuko Miyaguchi /
Abstract: Sodium-glucose cotransporter 2 (SGLT2) is imporant in glucose reabsorption. SGLT2 inhibitors suppress renal glucose reabsorption, therefore reducing blood glucose levels in patients with type 2 ...Sodium-glucose cotransporter 2 (SGLT2) is imporant in glucose reabsorption. SGLT2 inhibitors suppress renal glucose reabsorption, therefore reducing blood glucose levels in patients with type 2 diabetes. We and others have developed several SGLT2 inhibitors starting from phlorizin, a natural product. Using cryo-electron microscopy, we present the structures of human (h)SGLT2-MAP17 complexed with five natural or synthetic inhibitors. The four synthetic inhibitors (including canagliflozin) bind the transporter in the outward conformations, while phlorizin binds it in the inward conformation. The phlorizin-hSGLT2 interaction exhibits biphasic kinetics, suggesting that phlorizin alternately binds to the extracellular and intracellular sides. The Na-bound outward-facing and unbound inward-open structures of hSGLT2-MAP17 suggest that the MAP17-associated bundle domain functions as a scaffold, with the hash domain rotating around the Na-binding site. Thus, Na binding stabilizes the outward-facing conformation, and its release promotes state transition to inward-open conformation, exhibiting a role of Na in symport mechanism. These results provide structural evidence for the Na-coupled alternating-access mechanism proposed for the transporter family.
History
DepositionOct 27, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name
Revision 1.2Dec 20, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Feb 7, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,1545
Polymers85,4832
Non-polymers6723
Water724
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area990 Å2
ΔGint-9 kcal/mol
Surface area24050 Å2

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 73247.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC5A2, SGLT2 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P31639
#2: Protein PDZK1-interacting protein 1 / 17 kDa membrane-associated protein


Mass: 12235.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP17 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q13113

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Sugars , 1 types, 1 molecules

#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 6 molecules

#4: Chemical ChemComp-KZ3 / (2R,3R,4S,5S,6R)-2-[3-[(4-cyclopropylphenyl)methyl]-4-fluoranyl-indol-1-yl]-6-(hydroxymethyl)oxane-3,4,5-triol


Mass: 427.465 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H26FNO5 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: Binary complex of Sodium/glucose cotransporter 2 with PDZK1-interacting protein 1.
Type: COMPLEX
Details: Electrogenic Na+-coupled sugar simporter that actively transports D-glucose at the plasma membrane, with a Na+ to sugar coupling ratio of 1:1. Transporter activity is driven by a ...Details: Electrogenic Na+-coupled sugar simporter that actively transports D-glucose at the plasma membrane, with a Na+ to sugar coupling ratio of 1:1. Transporter activity is driven by a transmembrane Na+ electrochemical gradient set by the Na+/K+ pump
Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 64 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: REFMAC / Version: 5.8.0267 / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 103853 / Symmetry type: POINT
RefinementResolution: 2.9→2.9 Å / Cor.coef. Fo:Fc: 0.788 / SU B: 6.902 / SU ML: 0.137 / ESU R: 0.214
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.36392 --
obs0.36392 98512 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 65.913 Å2
Refinement stepCycle: 1 / Total: 4778
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0130.0134909
ELECTRON MICROSCOPYr_bond_other_d0.0290.0174752
ELECTRON MICROSCOPYr_angle_refined_deg2.0161.6236703
ELECTRON MICROSCOPYr_angle_other_deg1.4761.56210860
ELECTRON MICROSCOPYr_dihedral_angle_1_deg7.245612
ELECTRON MICROSCOPYr_dihedral_angle_2_deg28.87220202
ELECTRON MICROSCOPYr_dihedral_angle_3_deg15.16515747
ELECTRON MICROSCOPYr_dihedral_angle_4_deg16.7131529
ELECTRON MICROSCOPYr_chiral_restr0.0950.2627
ELECTRON MICROSCOPYr_gen_planes_refined0.0040.025447
ELECTRON MICROSCOPYr_gen_planes_other0.0010.021185
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it7.9636.3712457
ELECTRON MICROSCOPYr_mcbond_other7.9596.3642456
ELECTRON MICROSCOPYr_mcangle_it11.2069.6133066
ELECTRON MICROSCOPYr_mcangle_other11.2069.6213067
ELECTRON MICROSCOPYr_scbond_it9.4387.5452452
ELECTRON MICROSCOPYr_scbond_other9.4367.5512453
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other14.23210.9383635
ELECTRON MICROSCOPYr_long_range_B_refined19.32621146
ELECTRON MICROSCOPYr_long_range_B_other19.32521145
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.701 7275 -
obs--100 %

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