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- PDB-6ksw: Cryo-EM structure of the human concentrative nucleoside transport... -

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Basic information

Entry
Database: PDB / ID: 6ksw
TitleCryo-EM structure of the human concentrative nucleoside transporter CNT3
ComponentsSolute carrier family 28 member 3
KeywordsTRANSPORT PROTEIN / nucleoside / trimer / sodium symporter / SLC
Function / homology
Function and homology information


nucleoside:sodium symporter activity / pyrimidine-containing compound transmembrane transport / purine nucleobase transmembrane transport / uridine transmembrane transport / nucleoside transmembrane transport / Transport of nucleosides and free purine and pyrimidine bases across the plasma membrane / purine nucleobase transmembrane transporter activity / purine-specific nucleoside:sodium symporter activity / pyrimidine nucleoside transport / pyrimidine- and adenosine-specific:sodium symporter activity ...nucleoside:sodium symporter activity / pyrimidine-containing compound transmembrane transport / purine nucleobase transmembrane transport / uridine transmembrane transport / nucleoside transmembrane transport / Transport of nucleosides and free purine and pyrimidine bases across the plasma membrane / purine nucleobase transmembrane transporter activity / purine-specific nucleoside:sodium symporter activity / pyrimidine nucleoside transport / pyrimidine- and adenosine-specific:sodium symporter activity / purine nucleoside transmembrane transport / uridine transmembrane transporter activity / Ribavirin ADME / xenobiotic transmembrane transport / Azathioprine ADME / xenobiotic metabolic process / brush border membrane / endoplasmic reticulum membrane / plasma membrane
Similarity search - Function
Concentrative nucleoside transporter N-terminal domain / Concentrative nucleoside transporter / Concentrative nucleoside transporter C-terminal domain / Concentrative nucleoside transporter, metazoan/bacterial / Na+ dependent nucleoside transporter N-terminus / Na+ dependent nucleoside transporter C-terminus / Nucleoside transporter/FeoB GTPase, Gate domain / Nucleoside recognition
Similarity search - Domain/homology
Solute carrier family 28 member 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsZhou, Y.X. / Liao, L.H. / Li, J.L. / Xiao, Q.J. / Sun, L.F. / Deng, D.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2016YFA0502700 China
CitationJournal: PLoS Biol / Year: 2020
Title: Cryo-EM structure of the human concentrative nucleoside transporter CNT3.
Authors: Yanxia Zhou / Lianghuan Liao / Chen Wang / Jialu Li / Pengliang Chi / Qingjie Xiao / Qingting Liu / Li Guo / Linfeng Sun / Dong Deng /
Abstract: Concentrative nucleoside transporters (CNTs), members of the solute carrier (SLC) 28 transporter family, facilitate the salvage of nucleosides and therapeutic nucleoside derivatives across the plasma ...Concentrative nucleoside transporters (CNTs), members of the solute carrier (SLC) 28 transporter family, facilitate the salvage of nucleosides and therapeutic nucleoside derivatives across the plasma membrane. Despite decades of investigation, the structures of human CNTs remain unknown. We determined the cryogenic electron microscopy (cryo-EM) structure of human CNT (hCNT) 3 at an overall resolution of 3.6 Å. As with its bacterial homologs, hCNT3 presents a trimeric architecture with additional N-terminal transmembrane helices to stabilize the conserved central domains. The conserved binding sites for the substrate and sodium ions unravel the selective nucleoside transport and distinct coupling mechanism. Structural comparison of hCNT3 with bacterial homologs indicates that hCNT3 is stabilized in an inward-facing conformation. This study provides the molecular determinants for the transport mechanism of hCNTs and potentially facilitates the design of nucleoside drugs.
History
DepositionAug 26, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
C: Solute carrier family 28 member 3
A: Solute carrier family 28 member 3
B: Solute carrier family 28 member 3


Theoretical massNumber of molelcules
Total (without water)211,1103
Polymers211,1103
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Solute carrier family 28 member 3 / Concentrative Na(+)-nucleoside cotransporter 3 / hCNT3


Mass: 70370.109 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC28A3, CNT3 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9HAS3

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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: Trimer of a membrane protein / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 8
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 FIELD
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 99489 / Symmetry type: POINT

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