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Yorodumi- EMDB-32619: Structure of PfNT1(Y190A) in complex with nanobody 48 and inosine -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32619 | |||||||||
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Title | Structure of PfNT1(Y190A) in complex with nanobody 48 and inosine | |||||||||
Map data | ||||||||||
Sample |
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Keywords | malaria / Equilibrative nucleoside transporter / inosine / TRANSPORT PROTEIN | |||||||||
Function / homology | nicotinamide riboside transmembrane transporter activity / Equilibrative nucleoside transporter / nucleobase transmembrane transporter activity / MFS transporter superfamily / membrane / Equilibrative nucleoside/nucleobase transporter Function and homology information | |||||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) / Vicugna pacos (alpaca) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.11 Å | |||||||||
Authors | Wang C / Deng D | |||||||||
Funding support | China, 2 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_32619.map.gz | 86 MB | EMDB map data format | |
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Header (meta data) | emd-32619-v30.xml emd-32619.xml | 12.5 KB 12.5 KB | Display Display | EMDB header |
Images | emd_32619.png | 105.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32619 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32619 | HTTPS FTP |
-Validation report
Summary document | emd_32619_validation.pdf.gz | 501.6 KB | Display | EMDB validaton report |
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Full document | emd_32619_full_validation.pdf.gz | 501.1 KB | Display | |
Data in XML | emd_32619_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | emd_32619_validation.cif.gz | 7.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32619 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32619 | HTTPS FTP |
-Related structure data
Related structure data | 7wn1MC 7wn0C 7ydqC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_32619.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Structure of PfNT1(Y190A) in complex with nanobody 48 and inosine
Entire | Name: Structure of PfNT1(Y190A) in complex with nanobody 48 and inosine |
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Components |
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-Supramolecule #1: Structure of PfNT1(Y190A) in complex with nanobody 48 and inosine
Supramolecule | Name: Structure of PfNT1(Y190A) in complex with nanobody 48 and inosine type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Plasmodium falciparum (malaria parasite P. falciparum) |
-Supramolecule #2: PfNT1
Supramolecule | Name: PfNT1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Vicugna pacos (alpaca) |
-Supramolecule #3: nanobody 48
Supramolecule | Name: nanobody 48 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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-Macromolecule #1: Equilibrative nucleoside/nucleobase transporter
Macromolecule | Name: Equilibrative nucleoside/nucleobase transporter / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Plasmodium falciparum (malaria parasite P. falciparum) |
Molecular weight | Theoretical: 47.579801 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MSTGKESSKA YADIESRGDY KDDGKKGSTL SSKQHFMLSL TFILIGLSSL NVWNTALGLN INFKYNTFQI TGLVCSSIVA LFVEIPKIM LPFLLGGLSI LCAGFQISHS FFTDTQFDTY CLVAFIVIGV VAGLAQTIAF NIGSTMEDNM GGYMSAGIGI S GVFIFVIN ...String: MSTGKESSKA YADIESRGDY KDDGKKGSTL SSKQHFMLSL TFILIGLSSL NVWNTALGLN INFKYNTFQI TGLVCSSIVA LFVEIPKIM LPFLLGGLSI LCAGFQISHS FFTDTQFDTY CLVAFIVIGV VAGLAQTIAF NIGSTMEDNM GGYMSAGIGI S GVFIFVIN LLLDQFVSPE KHYGVNKAKL LALYIICELC LILAIVFCVC NLDLTNKNNK KDEENKENNA TLSYMELFKD SY KAILTMF LVNWLTLQLF PGVGHKKWQE SHNISDYNVT IIVGMFQVFD FLSRYPPNLT HIKIFKNFTF SLNKLLVANS LRL LFIPWF ILNACVDHPF FKNIVQQCVC MAMLAFTNGW FNTVPFLVFV KELKKAKKKK EIEIISTFLV IAMFVGLFCG IWTT YIYNL FNIVLPKPDL PPIDVTQ UniProtKB: Equilibrative nucleoside/nucleobase transporter |
-Macromolecule #2: nanobody48
Macromolecule | Name: nanobody48 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Vicugna pacos (alpaca) |
Molecular weight | Theoretical: 13.199559 KDa |
Recombinant expression | Organism: Bacillus subtilis (bacteria) |
Sequence | String: QVQLVESGGG LVQPGGSLRL SCAASGFTGS INYMGWYRQA PGKQRELVAR FSSGGSTNYA DSVKGRFTIS GDNAKNTVYL QMNSLKPED TAVYYCNAET ISYVYTVVFQ DYWGQGTQVT VSS |
-Macromolecule #3: INOSINE
Macromolecule | Name: INOSINE / type: ligand / ID: 3 / Number of copies: 1 / Formula: NOS |
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Molecular weight | Theoretical: 268.226 Da |
Chemical component information | ChemComp-NOS: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 6 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 56.3 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 183797 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |