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- EMDB-0775: Cryo-EM structure of the human concentrative nucleoside transport... -

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Basic information

Entry
Database: EMDB / ID: EMD-0775
TitleCryo-EM structure of the human concentrative nucleoside transporter CNT3
Map data
Sample
  • Complex: Trimer of a membrane protein
    • Protein or peptide: Solute carrier family 28 member 3
Keywordsnucleoside / trimer / sodium symporter / SLC / TRANSPORT PROTEIN
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
Concentrative nucleoside transporter CNT3 / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsZhou YX / Liao LH
Funding support China, 1 items
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, 2019-
Header (metadata) releaseAug 26, 2020-
Map releaseAug 26, 2020-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ksw
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0775.png

Downloads & links

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Map

FileDownload / File: emd_0775.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.04 Å
Density
Contour LevelBy AUTHOR: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.13439864 - 0.24454413
Average (Standard dev.)0.00051492744 (±0.008860232)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 249.59999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z249.600249.600249.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.1340.2450.001

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Supplemental data

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Sample components

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Entire : Trimer of a membrane protein

EntireName: Trimer of a membrane protein
Components
  • Complex: Trimer of a membrane protein
    • Protein or peptide: Solute carrier family 28 member 3

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Supramolecule #1: Trimer of a membrane protein

SupramoleculeName: Trimer of a membrane protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Solute carrier family 28 member 3

MacromoleculeName: Solute carrier family 28 member 3 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 70.370109 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MEDDDEEMQQ KGCLERRYDT VCGFCRKHKT TLRHIIWGIL LAGYLVMVIS ACVLNFHRAL PLFVITVAAI FFVVWDHLMA KYEHRIDEM LSPGRRLLNS HWFWLKWVIW SSLVLAVIFW LAFDTAKLGQ QQLVSFGGLI MYIVLLFLFS KYPTRVYWRP V LWGIGLQF ...String:
MEDDDEEMQQ KGCLERRYDT VCGFCRKHKT TLRHIIWGIL LAGYLVMVIS ACVLNFHRAL PLFVITVAAI FFVVWDHLMA KYEHRIDEM LSPGRRLLNS HWFWLKWVIW SSLVLAVIFW LAFDTAKLGQ QQLVSFGGLI MYIVLLFLFS KYPTRVYWRP V LWGIGLQF LLGLLILRTD PGFIAFDWLG RQVQTFLEYT DAGASFVFGE KYKDHFFAFK VLPIVVFFST VMSMLYYLGL MQ WIIRKVG WIMLVTTGSS PIESVVASGN IFVGQTESPL LVRPYLPYIT KSELHAIMTA GFSTIAGSVL GAYISFGVPS SHL LTASVM SAPASLAAAK LFWPETEKPK ITLKNAMKME SGDSGNLLEA ATQGASSSIS LVANIAVNLI AFLALLSFMN SALS WFGNM FDYPQLSFEL ICSYIFMPFS FMMGVEWQDS FMVARLIGYK TFFNEFVAYE HLSKWIHLRK EGGPKFVNGV QQYIS IRSE IIATYALCGF ANIGSLGIVI GGLTSMAPSR KRDIASGAVR ALIAGTVACF MTACIAGILS STPVDINCHH VLENAF NST FPGNTTKVIA CCQSLLSSTV AKGPGEVIPG GNHSLYSLKG CCTLLNPSTF NCNGISNTFL EWSHPQFEK

UniProtKB: Solute carrier family 28 member 3

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 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

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 99489
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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