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- EMDB-25195: CryoEM structure of SMCT1 -

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Basic information

Entry
Database: EMDB / ID: EMD-25195
TitleCryoEM structure of SMCT1
Map datasodium monocarboxylate cotransporter
Sample
  • Complex: SMCT1 and nanobody complex
    • Protein or peptide: Sodium-coupled monocarboxylate transporter 1
    • Protein or peptide: nanobody Nb2
  • Ligand: butanoic acid
Function / homology
Function and homology information


acetate transport / propionate transmembrane transporter activity / propanoate transmembrane transport / passive transmembrane transporter activity / monocarboxylate:sodium symporter activity / nicotinate transport / : / lactate transport / organic acid:sodium symporter activity / Organic anion transport by SLC5/17/25 transporters ...acetate transport / propionate transmembrane transporter activity / propanoate transmembrane transport / passive transmembrane transporter activity / monocarboxylate:sodium symporter activity / nicotinate transport / : / lactate transport / organic acid:sodium symporter activity / Organic anion transport by SLC5/17/25 transporters / pyruvate transport / lactate transmembrane transporter activity / nitrate transmembrane transport / monocarboxylic acid transmembrane transporter activity / iodide transport / GINS complex / : / chloride transport / sodium ion transport / monoatomic ion transport / apical plasma membrane / apoptotic process / extracellular exosome / plasma membrane
Similarity search - Function
SMCT1, solute-binding domain / : / Sodium/solute symporter / Sodium/glucose symporter superfamily / Sodium:solute symporter family / Sodium:solute symporter family profile.
Similarity search - Domain/homology
Sodium-coupled monocarboxylate transporter 1
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsQu Q / Han L / Panova O / Feng L / Skiniotis G
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-
UpdateJan 26, 2022-
Current statusJan 26, 2022Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.037
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.037
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7sl9
  • Surface level: 0.037
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_25195.png

Downloads & links

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Map

FileDownload / File: emd_25195.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsodium monocarboxylate cotransporter
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 200 pix.
= 212. Å		1.06 Å/pix.
x 200 pix.
= 212. Å		1.06 Å/pix.
x 200 pix.
= 212. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.037 / Movie #1: 0.037
Minimum - Maximum-0.21009777 - 0.2996394
Average (Standard dev.)-0.00015502173 (±0.0068297293)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 211.99998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z212.000212.000212.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.2100.300-0.000

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Supplemental data

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Sample components

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Entire : SMCT1 and nanobody complex

EntireName: SMCT1 and nanobody complex
Components
  • Complex: SMCT1 and nanobody complex
    • Protein or peptide: Sodium-coupled monocarboxylate transporter 1
    • Protein or peptide: nanobody Nb2
  • Ligand: butanoic acid

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Supramolecule #1: SMCT1 and nanobody complex

SupramoleculeName: SMCT1 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-coupled monocarboxylate transporter 1

MacromoleculeName: Sodium-coupled monocarboxylate transporter 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 67.636219 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDTPRGIGTF VVWDYVVFAG MLVISAAIGI YYAFAGGGQQ TSKDFLMGGR RMTAVPVALS LTASFMSAVT VLGTPSEVYR FGAIFSIFA FTYFFVVVIS AEVFLPVFYK LGITSTYEYL ELRFNKCVRL CGTVLFIVQT ILYTGIVIYA PALALNQVTG F DLWGAVVA ...String:
MDTPRGIGTF VVWDYVVFAG MLVISAAIGI YYAFAGGGQQ TSKDFLMGGR RMTAVPVALS LTASFMSAVT VLGTPSEVYR FGAIFSIFA FTYFFVVVIS AEVFLPVFYK LGITSTYEYL ELRFNKCVRL CGTVLFIVQT ILYTGIVIYA PALALNQVTG F DLWGAVVA TGVVCTFYCT LGGLKAVIWT DVFQVGIMVA GFASVIIQAV VMQGGISTIL NDAYDGGRLN FWNFNPNPLQ RH TFWTIII GGTFTWTSIY GVNQSQVQRY ISCKSRFQAK LSLYINLVGL WAILTCSVFC GLALYSRYHD CDPWTAKKVS APD QLMPYL VLDILQDYPG LPGLFVACAY SGTLSTVSSS INALAAVTVE DLIKPYFRSL SERSLSWISQ GMSVVYGALC IGMA ALASL MGALLQAALS VFGMVGGPLM GLFALGILVP FANSIGALVG LMAGFAISLW VGIGAQIYPP LPERTLPLHL DIQGC NSTY NETNLMTTTE MPFTTSVFQI YNVQRTPLMD NWYSLSYLYF STVGTLVTLL VGILVSLSTG GRKQNLDPRY ILTKED FLS NFDIFKKKKH VLSYKSHPVE DGGTDNPAFN HIELNSDQSG KSNGTRLSNS LEVLFQ

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Macromolecule #2: nanobody Nb2

MacromoleculeName: nanobody Nb2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 14.441961 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MAQVQLQESG GGLVQAGGSL RLSCAASGNI STRAGMGWYR QAPGKEREFV ASINWGAITN YADSVKGRFT ISRDNAKNTV YLQMNSLKP EDTAVYYCAV EYKYGPQRSD TYYYWGQGTQ VTVSSHHHHH H

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Macromolecule #3: butanoic acid

MacromoleculeName: butanoic acid / type: ligand / ID: 3 / Number of copies: 1 / Formula: BUA
Molecular weightTheoretical: 88.105 Da
Chemical component information

ChemComp-BUA:
butanoic acid

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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 K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 56.0 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

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 173859
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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