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Yorodumi- PDB-6ksw: Cryo-EM structure of the human concentrative nucleoside transport... -
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-Basic information
Entry | Database: PDB / ID: 6ksw | ||||||
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Title | Cryo-EM structure of the human concentrative nucleoside transporter CNT3 | ||||||
Components | Solute carrier family 28 member 3 | ||||||
Keywords | TRANSPORT PROTEIN / nucleoside / trimer / sodium symporter / SLC | ||||||
Function / homology | Function and homology information nucleoside:sodium symporter activity / purine nucleobase transmembrane transport / pyrimidine-containing compound transmembrane transport / uridine transmembrane transport / Transport of nucleosides and free purine and pyrimidine bases across the plasma membrane / nucleoside transmembrane transport / nucleoside transmembrane transporter activity / purine nucleobase transmembrane transporter activity / uridine transmembrane transporter activity / pyrimidine- and adenosine-specific:sodium symporter activity ...nucleoside:sodium symporter activity / purine nucleobase transmembrane transport / pyrimidine-containing compound transmembrane transport / uridine transmembrane transport / Transport of nucleosides and free purine and pyrimidine bases across the plasma membrane / nucleoside transmembrane transport / nucleoside transmembrane transporter activity / purine nucleobase transmembrane transporter activity / uridine transmembrane transporter activity / pyrimidine- and adenosine-specific:sodium symporter activity / purine-specific nucleoside:sodium symporter activity / pyrimidine nucleoside transport / purine nucleoside transmembrane transport / symporter activity / plasma membrane => GO:0005886 / brush border membrane / endoplasmic reticulum membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||
Authors | Zhou, Y.X. / Liao, L.H. / Li, J.L. / Xiao, Q.J. / Sun, L.F. / Deng, D. | ||||||
Funding support | China, 1items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6ksw.cif.gz | 265 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ksw.ent.gz | 210.9 KB | Display | PDB format |
PDBx/mmJSON format | 6ksw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ksw_validation.pdf.gz | 913 KB | Display | wwPDB validaton report |
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Full document | 6ksw_full_validation.pdf.gz | 924.1 KB | Display | |
Data in XML | 6ksw_validation.xml.gz | 42.6 KB | Display | |
Data in CIF | 6ksw_validation.cif.gz | 65.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ks/6ksw ftp://data.pdbj.org/pub/pdb/validation_reports/ks/6ksw | HTTPS FTP |
-Related structure data
Related structure data | 0775MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | 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
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Trimer of a membrane protein / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 99489 / Symmetry type: POINT |