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- PDB-7sl9: CryoEM structure of SMCT1 -

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Basic information

Entry
Database: PDB / ID: 7sl9
TitleCryoEM structure of SMCT1
Components
  • Sodium-coupled monocarboxylate transporter 1
  • nanobody Nb2
KeywordsMEMBRANE PROTEIN / transporter / TRANSPORT PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


propionate transmembrane transporter activity / propanoate transmembrane transport / short-chain fatty acid transmembrane transport / passive transmembrane transporter activity / monocarboxylate:sodium symporter activity / Organic anion transporters / organic acid:sodium symporter activity / monocarboxylic acid transmembrane transporter activity / lactate transmembrane transporter activity / NAD biosynthesis via nicotinamide riboside salvage pathway ...propionate transmembrane transporter activity / propanoate transmembrane transport / short-chain fatty acid transmembrane transport / passive transmembrane transporter activity / monocarboxylate:sodium symporter activity / Organic anion transporters / organic acid:sodium symporter activity / monocarboxylic acid transmembrane transporter activity / lactate transmembrane transporter activity / NAD biosynthesis via nicotinamide riboside salvage pathway / Nicotinamide salvaging / symporter activity / sodium ion transport / monoatomic ion transport / membrane => GO:0016020 / 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
butanoic acid / Sodium-coupled monocarboxylate transporter 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsQu, Q. / Han, L. / Panova, O. / Feng, L. / Skiniotis, G.
Funding support1items
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, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 26, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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Structure visualization

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  • Deposited structure unit
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Sodium-coupled monocarboxylate transporter 1
B: nanobody Nb2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,1663
Polymers82,0782
Non-polymers881
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Sodium-coupled monocarboxylate transporter 1 / / Apical iodide transporter / Electrogenic sodium monocarboxylate cotransporter / Sodium iodide- ...Apical iodide transporter / Electrogenic sodium monocarboxylate cotransporter / Sodium iodide-related cotransporter / Solute carrier family 5 member 8


Mass: 67636.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC5A8, AIT, SMCT, SMCT1 / Production host: Homo sapiens (human) / References: UniProt: Q8N695
#2: Antibody nanobody Nb2


Mass: 14441.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Chemical ChemComp-BUA / butanoic acid / Butyric acid


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: SMCT1 and nanobody complex / Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 56 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 173859 / Symmetry type: POINT

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