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- PDB-9k7s: Structure of PfENT1(S143C,S382C) with inosine -

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Basic information

Entry
Database: PDB / ID: 9k7s
TitleStructure of PfENT1(S143C,S382C) with inosine
ComponentsNucleoside transporter 1
KeywordsTRANSPORT PROTEIN / complex / membrane protein / inosine
Function / homology
Function and homology information


Transport of nucleosides and free purine and pyrimidine bases across the plasma membrane / Ribavirin ADME / adenosine transport / Azathioprine ADME / nucleoside transmembrane transporter activity / purine nucleobase transport / plasma membrane
Similarity search - Function
Equilibrative nucleoside transporter / MFS transporter superfamily
Similarity search - Domain/homology
INOSINE / Nucleoside transporter 1
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.69 Å
AuthorsChen, X.Y. / Li, J.L. / Wang, X. / Deng, D.
Funding support China, 1items
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, X.Y. / Li, J.L. / Wang, X. / Deng, D.
History
DepositionOct 24, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 29, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleoside transporter 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8932
Polymers43,6251
Non-polymers2681
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Nucleoside transporter 1 / Equilibrative nucleoside transporter 1 / PfNT1 / Equilibrative nucleoside transporter type 1 / PfENT1


Mass: 43624.637 Da / Num. of mol.: 1 / Mutation: S143C,S382C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: NT1, PF3D7_1347200 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8IDM6
#2: Chemical ChemComp-NOS / INOSINE


Mass: 268.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N4O5 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: Structure of PfENT1(S143C,S382C) with inosine / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 47.5 kDa/nm / Experimental value: NO
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1100 nm
Image recordingElectron dose: 51.234 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.69 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 90255 / Symmetry type: POINT
RefinementHighest resolution: 3.69 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0023048
ELECTRON MICROSCOPYf_angle_d0.4964141
ELECTRON MICROSCOPYf_dihedral_angle_d11.421047
ELECTRON MICROSCOPYf_chiral_restr0.039490
ELECTRON MICROSCOPYf_plane_restr0.004497

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