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- EMDB-25196: CryoEM structure of SGLT1 at 3.15 angstrom resolution -

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Basic information

Entry
Database: EMDB / ID: EMD-25196
TitleCryoEM structure of SGLT1 at 3.15 angstrom resolution
Map data
Sample
  • Complex: SGLT1 and nanobody complex
    • Protein or peptide: Sodium/glucose cotransporter 1
    • Protein or peptide: nanobody Nb1
  • Ligand: CHOLESTEROL HEMISUCCINATE
KeywordsMembrane transporter / TRANSPORT PROTEIN-IMMUNE SYSTEM complex / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsQu Q / Han L
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nature / Year: 2022
Title: Structure and mechanism of the SGLT family of glucose transporters.
Authors: Lei Han / Qianhui Qu / Deniz Aydin / Ouliana Panova / Michael J Robertson / Yan Xu / Ron O Dror / Georgios Skiniotis / Liang Feng /
Abstract: Glucose is a primary energy source in living cells. The discovery in 1960s that a sodium gradient powers the active uptake of glucose in the intestine heralded the concept of a secondary active ...Glucose is a primary energy source in living cells. The discovery in 1960s that a sodium gradient powers the active uptake of glucose in the intestine heralded the concept of a secondary active transporter that can catalyse the movement of a substrate against an electrochemical gradient by harnessing energy from another coupled substrate. Subsequently, coupled Na/glucose transport was found to be mediated by sodium-glucose cotransporters (SGLTs). SGLTs are responsible for active glucose and galactose absorption in the intestine and for glucose reabsorption in the kidney, and are targeted by multiple drugs to treat diabetes. Several members within the SGLT family transport key metabolites other than glucose. Here we report cryo-electron microscopy structures of the prototypic human SGLT1 and a related monocarboxylate transporter SMCT1 from the same family. The structures, together with molecular dynamics simulations and functional studies, define the architecture of SGLTs, uncover the mechanism of substrate binding and selectivity, and shed light on water permeability of SGLT1. These results provide insights into the multifaceted functions of SGLTs.
History
DepositionOct 23, 2021-
Header (metadata) releaseDec 15, 2021-
Map releaseDec 15, 2021-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.37
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.37
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7sla
  • Surface level: 0.37
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_25196.png

Downloads & links

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Map

FileDownload / File: emd_25196.map.gz / Format: CCP4 / Size: 107.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 304 pix.
= 258.4 Å		0.85 Å/pix.
x 304 pix.
= 258.4 Å		0.85 Å/pix.
x 304 pix.
= 258.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.37 / Movie #1: 0.37
Minimum - Maximum-1.9844781 - 3.1811075
Average (Standard dev.)-0.0022151829 (±0.07107958)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions304304304
Spacing304304304
CellA=B=C: 258.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.850.850.85
M x/y/z304304304
origin x/y/z0.0000.0000.000
length x/y/z258.400258.400258.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS304304304
D min/max/mean-1.9843.181-0.002

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Supplemental data

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Sample components

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Entire : SGLT1 and nanobody complex

EntireName: SGLT1 and nanobody complex
Components
  • Complex: SGLT1 and nanobody complex
    • Protein or peptide: Sodium/glucose cotransporter 1
    • Protein or peptide: nanobody Nb1
  • Ligand: CHOLESTEROL HEMISUCCINATE

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Supramolecule #1: SGLT1 and nanobody complex

SupramoleculeName: SGLT1 and nanobody 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: 74.622031 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDSSTWSPKT TAVTRPVETH ELIRNAADIS VIVIYFLLVM AVGLWSMFKT NRGTVGGFFL AGRSMVWWPI GASLFASNIG SGHFIGLAG TGAASGLAVG GFEWNALVLL LVLGWVFVPI YIKAGVVTMP EYLRKRFGGQ RIQVYLSVLS LFLYIFTKIS V DIFSGAIF ...String:
MDSSTWSPKT TAVTRPVETH ELIRNAADIS VIVIYFLLVM AVGLWSMFKT NRGTVGGFFL AGRSMVWWPI GASLFASNIG SGHFIGLAG TGAASGLAVG GFEWNALVLL LVLGWVFVPI YIKAGVVTMP EYLRKRFGGQ RIQVYLSVLS LFLYIFTKIS V DIFSGAIF INLALGWNLY LSIILLLAIT ALYTITGGLA AVIYTDTLQT LIMLIGALIL MGFAFHEVGG YDAFMEKYMK AI PTIVSDG NTTFQEKCYT PRADSFHIFR DPLTGDLPWP GFIFGLTILA LWYWCTDQVI VQRCLAAKNM SHVKGGCILA GYL KLLPMF IMVMPGMISR ILFPDKVACV VPSECEKYCG TKVGCTNIAY PTLVVELMPN GLRGLMLAVM LAALMSSLTS IFNS ASTLF TMDIYAKVRK RASEKELMIV GRLFVLFLVV VSIAWIPIVQ SAQSGQLFDY IQSVSSYLAP PVAAVFLLAI FWKRV NEQG AFWGLILGLL LGLSRLILEF AYGTGSCMEP SNCPTIICGV HYLYFAIILF AISGIVTVVV SLLTKPIPDV HLYRLC WSL RNSKEERIDL DAEEENIQEG PKETIEIETQ VPEKKKGIFR RAYDLFCGLE QHGAPKMTEE EEKAMKMKMT DTSEKPL WR TVLNINAILL LAVAIFCHAY FASNSLEVLF Q

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Macromolecule #2: nanobody Nb1

MacromoleculeName: nanobody Nb1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 14.126768 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MAQVQLQESG GGLVQAGGSL RLSCAASGTI FVFDKMGWYR QAPGKEREFV ATISRGGSTN YADSVKGRFT ISRDNAKNTV YLQMNSLKP EDTAVYYCAV RYTPWRRYSY WGQGTQVTVS SHHHHHH

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Macromolecule #3: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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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
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: 67.88 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 94369
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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