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- PDB-9k8y: Structure of PfENT1(T144C,K375C,N60R,Q266R) with inosine- outward... -

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Basic information

Entry
Database: PDB / ID: 9k8y
TitleStructure of PfENT1(T144C,K375C,N60R,Q266R) with inosine- outward-facing state
ComponentsNucleoside transporter 1
KeywordsTRANSPORT PROTEIN / complex / membrane protein / inosine
Function / homologyadenosine transport / Equilibrative nucleoside transporter / nucleoside transmembrane transporter activity / purine nucleobase transport / MFS transporter superfamily / plasma membrane / INOSINE / Nucleoside transporter 1
Function and homology information
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.76 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(T144C,K375C,N60R,Q266R) with inosine- outward-facing state
Authors: Chen, X.Y. / Li, J.L. / Wang, X. / Deng, D.
History
DepositionOct 25, 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)42,9412
Polymers42,6721
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: 42672.457 Da / Num. of mol.: 1 / Mutation: T144C,K375C,N60R,Q266R
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(T144C,K375C,N60R,Q266R) with inosine- outward-facing state
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 47.5 kDa/nm / Experimental value: YES
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

CTF correctionType: NONE
3D reconstructionResolution: 3.76 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 102309 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0032977
ELECTRON MICROSCOPYf_angle_d0.5314042
ELECTRON MICROSCOPYf_dihedral_angle_d10.9281020
ELECTRON MICROSCOPYf_chiral_restr0.039477
ELECTRON MICROSCOPYf_plane_restr0.004484

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