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Yorodumi- PDB-7wn1: Structure of PfNT1(Y190A) in complex with nanobody 48 and inosine -
+Open data
-Basic information
Entry | Database: PDB / ID: 7wn1 | |||||||||
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Title | Structure of PfNT1(Y190A) in complex with nanobody 48 and inosine | |||||||||
Components |
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Keywords | TRANSPORT PROTEIN / malaria / Equilibrative nucleoside transporter / inosine | |||||||||
Function / homology | nicotinamide riboside transmembrane transporter activity / Equilibrative nucleoside transporter / nucleobase transmembrane transporter activity / fungal-type vacuole membrane / MFS transporter superfamily / INOSINE / Equilibrative nucleoside/nucleobase transporter Function and homology information | |||||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) Vicugna pacos (alpaca) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.11 Å | |||||||||
Authors | Wang, C. / Deng, D. / Ren, R.B. / Yu, L.Y. | |||||||||
Funding support | China, 2items
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Citation | Journal: Nat Commun / Year: 2023 Title: Structural basis of the substrate recognition and inhibition mechanism of Plasmodium falciparum nucleoside transporter PfENT1. Authors: Chen Wang / Leiye Yu / Jiying Zhang / Yanxia Zhou / Bo Sun / Qingjie Xiao / Minhua Zhang / Huayi Liu / Jinhong Li / Jialu Li / Yunzi Luo / Jie Xu / Zhong Lian / Jingwen Lin / Xiang Wang / ...Authors: Chen Wang / Leiye Yu / Jiying Zhang / Yanxia Zhou / Bo Sun / Qingjie Xiao / Minhua Zhang / Huayi Liu / Jinhong Li / Jialu Li / Yunzi Luo / Jie Xu / Zhong Lian / Jingwen Lin / Xiang Wang / Peng Zhang / Li Guo / Ruobing Ren / Dong Deng / Abstract: By lacking de novo purine biosynthesis enzymes, Plasmodium falciparum requires purine nucleoside uptake from host cells. The indispensable nucleoside transporter ENT1 of P. falciparum facilitates ...By lacking de novo purine biosynthesis enzymes, Plasmodium falciparum requires purine nucleoside uptake from host cells. The indispensable nucleoside transporter ENT1 of P. falciparum facilitates nucleoside uptake in the asexual blood stage. Specific inhibitors of PfENT1 prevent the proliferation of P. falciparum at submicromolar concentrations. However, the substrate recognition and inhibitory mechanism of PfENT1 are still elusive. Here, we report cryo-EM structures of PfENT1 in apo, inosine-bound, and inhibitor-bound states. Together with in vitro binding and uptake assays, we identify that inosine is the primary substrate of PfENT1 and that the inosine-binding site is located in the central cavity of PfENT1. The endofacial inhibitor GSK4 occupies the orthosteric site of PfENT1 and explores the allosteric site to block the conformational change of PfENT1. Furthermore, we propose a general "rocker switch" alternating access cycle for ENT transporters. Understanding the substrate recognition and inhibitory mechanisms of PfENT1 will greatly facilitate future efforts in the rational design of antimalarial drugs. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wn1.cif.gz | 98.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wn1.ent.gz | 72.1 KB | Display | PDB format |
PDBx/mmJSON format | 7wn1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wn1_validation.pdf.gz | 889.9 KB | Display | wwPDB validaton report |
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Full document | 7wn1_full_validation.pdf.gz | 894.9 KB | Display | |
Data in XML | 7wn1_validation.xml.gz | 21.2 KB | Display | |
Data in CIF | 7wn1_validation.cif.gz | 29.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wn/7wn1 ftp://data.pdbj.org/pub/pdb/validation_reports/wn/7wn1 | HTTPS FTP |
-Related structure data
Related structure data | 32619MC 7wn0C 7ydqC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 47579.801 Da / Num. of mol.: 1 / Mutation: Y190A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Gene: NT1, ENT1 / Cell line (production host): IPLB-Sf-21-AE(Sf9) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9NIH7 |
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#2: Antibody | Mass: 13199.559 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Bacillus subtilis (bacteria) |
#3: Chemical | ChemComp-NOS / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Source (recombinant) |
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Buffer solution | pH: 6 | ||||||||||||||||||||||||
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 / Nominal defocus max: 1800 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 56.3 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19_4092: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 183797 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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