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- EMDB-33962: Structure of human SGLT1-MAP17 complex bound with substrate 4D4FD... -

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Basic information

Entry
Database: EMDB / ID: EMD-33962
TitleStructure of human SGLT1-MAP17 complex bound with substrate 4D4FDG in the occluded conformation
Map data
Sample
  • Complex: human SGLT1-MAP17 complex
    • Protein or peptide: Sodium/glucose cotransporter 1
    • Protein or peptide: PDZK1-interacting protein 1
  • Ligand: (2R,3R,4R,5S,6R)-5-fluoranyl-6-(hydroxymethyl)oxane-2,3,4-triol
Keywordsglucose transporter / SGLT / sodium glucose transporter / membrane protein / PROTEIN TRANSPORT
Function / homology
Function and homology information


myo-inositol:sodium symporter activity / pentose transmembrane transporter activity / galactose:sodium symporter activity / pentose transmembrane transport / myo-inositol transport / intestinal hexose absorption / Defective SLC5A1 causes congenital glucose/galactose malabsorption (GGM) / Intestinal hexose absorption / fucose transmembrane transport / fucose transmembrane transporter activity ...myo-inositol:sodium symporter activity / pentose transmembrane transporter activity / galactose:sodium symporter activity / pentose transmembrane transport / myo-inositol transport / intestinal hexose absorption / Defective SLC5A1 causes congenital glucose/galactose malabsorption (GGM) / Intestinal hexose absorption / fucose transmembrane transport / fucose transmembrane transporter activity / intestinal D-glucose absorption / galactose transmembrane transporter activity / galactose transmembrane transport / alpha-glucoside transport / alpha-glucoside transmembrane transporter activity / D-glucose:sodium symporter activity / water transmembrane transporter activity / renal D-glucose absorption / D-glucose import across plasma membrane / Cellular hexose transport / D-glucose transmembrane transporter activity / D-glucose transmembrane transport / transepithelial water transport / sodium ion import across plasma membrane / sodium ion transport / intracellular vesicle / transport across blood-brain barrier / brush border membrane / nuclear membrane / early endosome / apical plasma membrane / perinuclear region of cytoplasm / Golgi apparatus / extracellular exosome / 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 1 / PDZK1-interacting protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsChen L / Niu Y / Cui W
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)91957201 China
National Natural Science Foundation of China (NSFC)31821091 China
National Natural Science Foundation of China (NSFC)31870833 China
CitationJournal: Nat Commun / Year: 2023
Title: Structures of human SGLT in the occluded state reveal conformational changes during sugar transport.
Authors: Wenhao Cui / Yange Niu / Zejian Sun / Rui Liu / Lei Chen /
Abstract: Sodium-Glucose Cotransporters (SGLT) mediate the uphill uptake of extracellular sugars and play fundamental roles in sugar metabolism. Although their structures in inward-open and outward-open ...Sodium-Glucose Cotransporters (SGLT) mediate the uphill uptake of extracellular sugars and play fundamental roles in sugar metabolism. Although their structures in inward-open and outward-open conformations are emerging from structural studies, the trajectory of how SGLTs transit from the outward-facing to the inward-facing conformation remains unknown. Here, we present the cryo-EM structures of human SGLT1 and SGLT2 in the substrate-bound state. Both structures show an occluded conformation, with not only the extracellular gate but also the intracellular gate tightly sealed. The sugar substrate are caged inside a cavity surrounded by TM1, TM2, TM3, TM6, TM7, and TM10. Further structural analysis reveals the conformational changes associated with the binding and release of substrates. These structures fill a gap in our understanding of the structural mechanisms of SGLT transporters.
History
DepositionJul 31, 2022-
Header (metadata) releaseMay 31, 2023-
Map releaseMay 31, 2023-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33962.png

Downloads & links

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Map

FileDownload / File: emd_33962.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 240 pix.
= 200.16 Å		0.83 Å/pix.
x 240 pix.
= 200.16 Å		0.83 Å/pix.
x 240 pix.
= 200.16 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.834 Å
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Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-5.2238383 - 6.6582437
Average (Standard dev.)0.008971879 (±0.14588022)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 200.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_33962_msk_1.map
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Additional map: #1

Fileemd_33962_additional_1.map
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Half map: #2

Fileemd_33962_half_map_1.map
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Half map: #1

Fileemd_33962_half_map_2.map
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Sample components

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Entire : human SGLT1-MAP17 complex

EntireName: human SGLT1-MAP17 complex
Components
  • Complex: human SGLT1-MAP17 complex
    • Protein or peptide: Sodium/glucose cotransporter 1
    • Protein or peptide: PDZK1-interacting protein 1
  • Ligand: (2R,3R,4R,5S,6R)-5-fluoranyl-6-(hydroxymethyl)oxane-2,3,4-triol

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Supramolecule #1: human SGLT1-MAP17 complex

SupramoleculeName: human SGLT1-MAP17 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Sodium/glucose cotransporter 1

MacromoleculeName: Sodium/glucose cotransporter 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 73.557703 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDSSTWSPKT TAVTRPVETH ELIRNAADIS IIVIYFVVVM AVGLWAMFST NRGTVGGFFL AGRSMVWWPI GASLFASNIG SGHFVGLAG TGAASGIAIG GFEWNALVLV VVLGWLFVPI YIKAGVVTMP EYLRKRFGGQ RIQVYLSLLS LLLYIFTKIS A DIFSGAIF ...String:
MDSSTWSPKT TAVTRPVETH ELIRNAADIS IIVIYFVVVM AVGLWAMFST NRGTVGGFFL AGRSMVWWPI GASLFASNIG SGHFVGLAG TGAASGIAIG GFEWNALVLV VVLGWLFVPI YIKAGVVTMP EYLRKRFGGQ RIQVYLSLLS LLLYIFTKIS A DIFSGAIF INLALGLNLY LAIFLLLAIT ALYTITGGLA AVIYTDTLQT VIMLVGSLIL TGFAFHEVGG YDAFMEKYMK AI PTIVSDG NTTFQEKCYT PRADSFHIFR DPLTGDLPWP GFIFGMSILT LWYWCTDQVI VQRCLSAKNM SHVKGGCILC GYL KLMPMF IMVMPGMISR ILYTEKIACV VPSECEKYCG TKVGCTNIAY PTLVVELMPN GLRGLMLSVM LASLMSSLTS IFNS ASTLF TMDIYAKVRK RASEKELMIA GRLFILVLIG ISIAWVPIVQ SAQSGQLFDY IQSITSYLGP PIAAVFLLAI FWKRV NEPG AFWGLILGLL IGISRMITEF AYGTGSCMEP SNCPTIICGV HYLYFAIILF AISFITIVVI SLLTKPIPDV HLYRLC WSL RNSKEERIDL DAEEENIQEG PKETIEIETQ VPEKKKGIFR RAYDLFCGLE QHGAPKMTEE EEKAMKMKMT DTSEKPL WR TVLNVNGIIL VTVAVFCHAY FA

UniProtKB: Sodium/glucose cotransporter 1

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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: 12.235 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MSALSLLILG LLTAVPPASC QQGLGNLQPW MQGLIAVAVF LVLVAIAFAV NHFWCQEEPE PAHMILTVGN KADGVLVGTD GRYSSMAAS FRSSEHENAY ENVPEEEGKV RSTPM

UniProtKB: PDZK1-interacting protein 1

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Macromolecule #3: (2R,3R,4R,5S,6R)-5-fluoranyl-6-(hydroxymethyl)oxane-2,3,4-triol

MacromoleculeName: (2R,3R,4R,5S,6R)-5-fluoranyl-6-(hydroxymethyl)oxane-2,3,4-triol
type: ligand / ID: 3 / Number of copies: 1 / Formula: KQC
Molecular weightTheoretical: 182.147 Da
Chemical component information

ChemComp-KQC:
(2R,3R,4R,5S,6R)-5-fluoranyl-6-(hydroxymethyl)oxane-2,3,4-triol

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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

MicroscopeFEI TITAN 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

Startup modelType of model: NONE / Details: ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v3.1.0) / Number images used: 444691
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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