+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25194 | |||||||||
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Title | CryoEM structure of SGLT1 at 3.4 A resolution | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Homo sapiens (human) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Qu Q / Han L / Panova O / Feng L / Skiniotis G | |||||||||
Funding support | 1 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_25194.map.gz | 3.6 MB | EMDB map data format | |
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Header (meta data) | emd-25194-v30.xml emd-25194.xml | 11.2 KB 11.2 KB | Display Display | EMDB header |
Images | emd_25194.png | 51.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25194 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25194 | HTTPS FTP |
-Validation report
Summary document | emd_25194_validation.pdf.gz | 338.3 KB | Display | EMDB validaton report |
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Full document | emd_25194_full_validation.pdf.gz | 337.9 KB | Display | |
Data in XML | emd_25194_validation.xml.gz | 5.7 KB | Display | |
Data in CIF | emd_25194_validation.cif.gz | 6.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25194 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25194 | HTTPS FTP |
-Related structure data
Related structure data | 7sl8MC 7sl9C 7slaC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_25194.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : nanobody-SGLT complex
Entire | Name: nanobody-SGLT complex |
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Components |
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-Supramolecule #1: nanobody-SGLT complex
Supramolecule | Name: nanobody-SGLT complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Sodium/glucose cotransporter 1
Macromolecule | Name: Sodium/glucose cotransporter 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 74.65607 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 LAVAIFCWGY FASNSLEVLF Q |
-Macromolecule #2: nanobody Nb1
Macromolecule | Name: nanobody Nb1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 14.126768 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MAQVQLQESG GGLVQAGGSL RLSCAASGTI FVFDKMGWYR QAPGKEREFV ATISRGGSTN YADSVKGRFT ISRDNAKNTV YLQMNSLKP EDTAVYYCAV RYTPWRRYSY WGQGTQVTVS SHHHHHH |
-Macromolecule #3: CHOLESTEROL
Macromolecule | Name: CHOLESTEROL / type: ligand / ID: 3 / Number of copies: 1 / Formula: CLR |
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Molecular weight | Theoretical: 386.654 Da |
Chemical component information | ChemComp-CLR: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 56.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 262587 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |