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- EMDB-62152: Structure of PfENT1(S143C,S382C) with inosine -

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Basic information

Entry
Database: EMDB / ID: EMD-62152
TitleStructure of PfENT1(S143C,S382C) with inosine
Map data
Sample
  • Complex: Structure of PfENT1(S143C,S382C) with inosine
    • Protein or peptide: Nucleoside transporter 1
  • Ligand: INOSINE
Keywordscomplex / membrane protein / inosine / TRANSPORT PROTEIN
Function / homologyadenosine transport / Equilibrative nucleoside transporter / nucleoside transmembrane transporter activity / purine nucleobase transport / MFS transporter superfamily / plasma membrane / Nucleoside transporter 1
Function and homology information
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.69 Å
AuthorsChen XY / Li JL / Wang X / Deng D
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)3217110258 China
CitationJournal: To Be Published
Title: Structure of PfENT1(S143C,S382C) with inosine
Authors: Chen XY / Li JL / Wang X / Deng D
History
DepositionOct 24, 2024-
Header (metadata) releaseApr 29, 2026-
Map releaseApr 29, 2026-
UpdateApr 29, 2026-
Current statusApr 29, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62152.png

Downloads & links

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Map

FileDownload / File: emd_62152.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.0017419665 - 2.3400235
Average (Standard dev.)0.00039693635 (±0.015729804)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62152_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_62152_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Structure of PfENT1(S143C,S382C) with inosine

EntireName: Structure of PfENT1(S143C,S382C) with inosine
Components
  • Complex: Structure of PfENT1(S143C,S382C) with inosine
    • Protein or peptide: Nucleoside transporter 1
  • Ligand: INOSINE

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Supramolecule #1: Structure of PfENT1(S143C,S382C) with inosine

SupramoleculeName: Structure of PfENT1(S143C,S382C) with inosine / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)
Molecular weightTheoretical: 47.5 kDa/nm

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Macromolecule #1: Nucleoside transporter 1

MacromoleculeName: Nucleoside transporter 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)
Molecular weightTheoretical: 43.624637 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: LSSKQHFMLS LTFILIGLSS LNVWNTALGL NINFKYNTFQ ITGLVCSSIV ALFVEIPKIM LPFLLGGLSI LCAGFQISHS FFTDTQFDT YCLVAFIVIG VVAGLAQTIA FNIGCTMEDN MGGYMSAGIG ISGVFIFVIN LLLDQFVSPE KHYGVNKAKL L YLYIICEL ...String:
LSSKQHFMLS LTFILIGLSS LNVWNTALGL NINFKYNTFQ ITGLVCSSIV ALFVEIPKIM LPFLLGGLSI LCAGFQISHS FFTDTQFDT YCLVAFIVIG VVAGLAQTIA FNIGCTMEDN MGGYMSAGIG ISGVFIFVIN LLLDQFVSPE KHYGVNKAKL L YLYIICEL CLILAIVFCV CNLDLTNKNN KKDEENKENN ATLSYMELFK DSYKAILTMF LVNWLTLQLF PGVGHKKWQE SH NISDYNV TIIVGMFQVF DFLSRYPPNL THIKIFKNFT FSLNKLLVAN SLRLLFIPWF ILNACVDHPF FKNIVQQCVC MAM LAFTNG WFNTVPFLVF VKELKKAKKK KEIEIICTFL VIAMFVGLFC GIWTTYIYNL FNIVLPKP

UniProtKB: Nucleoside transporter 1

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Macromolecule #2: INOSINE

MacromoleculeName: INOSINE / type: ligand / ID: 2 / Number of copies: 1 / Formula: NOS
Molecular weightTheoretical: 268.226 Da
Chemical component information

ChemComp-NOS:
INOSINE

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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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 51.234 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.1 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.69 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 90255
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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