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- EMDB-33963: Structure of human SGLT2-MAP17 complex bound with substrate AMG i... -

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Basic information

Entry
Database: EMDB / ID: EMD-33963
TitleStructure of human SGLT2-MAP17 complex bound with substrate AMG in the occluded conformation
Map data
Sample
  • Complex: human SGLT2-MAP17 complex
    • Protein or peptide: Sodium/glucose cotransporter 2
    • Protein or peptide: PDZK1-interacting protein 1
  • Ligand: methyl alpha-D-glucopyranoside
Keywordsglucose transporter / SGLT / sodium glucose transporter / membrane protein / PROTEIN TRANSPORT
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
Sodium/glucose cotransporter 2 / PDZK1-interacting protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.33 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-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33963.png

Downloads & links

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Map

FileDownload / File: emd_33963.map.gz / Format: CCP4 / Size: 83.7 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.)
0.82 Å/pix.
x 280 pix.
= 229.88 Å		0.82 Å/pix.
x 280 pix.
= 229.88 Å		0.82 Å/pix.
x 280 pix.
= 229.88 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.821 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.616
Minimum - Maximum-3.1363854 - 4.0974884
Average (Standard dev.)0.0034966 (±0.075292625)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 229.87999 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_33963_msk_1.map
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Additional map: #2

Fileemd_33963_additional_1.map
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Additional map: #1

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Half map: #2

Fileemd_33963_half_map_1.map
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Half map: #1

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Sample components

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Entire : human SGLT2-MAP17 complex

EntireName: human SGLT2-MAP17 complex
Components
  • Complex: human SGLT2-MAP17 complex
    • Protein or peptide: Sodium/glucose cotransporter 2
    • Protein or peptide: PDZK1-interacting protein 1
  • Ligand: methyl alpha-D-glucopyranoside

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Supramolecule #1: human SGLT2-MAP17 complex

SupramoleculeName: human SGLT2-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 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: 12.235 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: methyl alpha-D-glucopyranoside

MacromoleculeName: methyl alpha-D-glucopyranoside / type: ligand / ID: 3 / Number of copies: 1 / Formula: GYP
Molecular weightTheoretical: 194.182 Da
Chemical component information

ChemComp-GYP:
methyl alpha-D-glucopyranoside

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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 K2 SUMMIT (4k 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: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 44391
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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