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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-30953 | |||||||||
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Title | Structure of PfFNT in complex with MMV007839 | |||||||||
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![]() | lactate transporter / TRANSPORT PROTEIN | |||||||||
Function / homology | ![]() high-affinity secondary active nitrite transmembrane transporter activity / lactate transmembrane transport / nitrite transport / lactate:proton symporter activity / formate transmembrane transporter activity / membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.29 Å | |||||||||
![]() | Yan CY / Jiang X / Peng X / Wang N / Zhu A / Xu H / Li J | |||||||||
![]() | ![]() Title: Structural characterization of the Plasmodium falciparum lactate transporter PfFNT alone and in complex with antimalarial compound MMV007839 reveals its inhibition mechanism. Authors: Xi Peng / Nan Wang / Angqi Zhu / Hanwen Xu / Jialu Li / Yanxia Zhou / Chen Wang / Qingjie Xiao / Li Guo / Fei Liu / Zhi-Jun Jia / Huaichuan Duan / Jianping Hu / Weidan Yuan / Jia Geng / ...Authors: Xi Peng / Nan Wang / Angqi Zhu / Hanwen Xu / Jialu Li / Yanxia Zhou / Chen Wang / Qingjie Xiao / Li Guo / Fei Liu / Zhi-Jun Jia / Huaichuan Duan / Jianping Hu / Weidan Yuan / Jia Geng / Chuangye Yan / Xin Jiang / Dong Deng / ![]() ![]() Abstract: Plasmodium falciparum, the deadliest causal agent of malaria, caused more than half of the 229 million malaria cases worldwide in 2019. The emergence and spreading of frontline drug-resistant ...Plasmodium falciparum, the deadliest causal agent of malaria, caused more than half of the 229 million malaria cases worldwide in 2019. The emergence and spreading of frontline drug-resistant Plasmodium strains are challenging to overcome in the battle against malaria and raise urgent demands for novel antimalarial agents. The P. falciparum formate-nitrite transporter (PfFNT) is a potential drug target due to its housekeeping role in lactate efflux during the intraerythrocytic stage. Targeting PfFNT, MMV007839 was identified as a lead compound that kills parasites at submicromolar concentrations. Here, we present 2 cryogenic-electron microscopy (cryo-EM) structures of PfFNT, one with the protein in its apo form and one with it in complex with MMV007839, both at 2.3 Å resolution. Benefiting from the high-resolution structures, our study provides the molecular basis for both the lactate transport of PfFNT and the inhibition mechanism of MMV007839, which facilitates further antimalarial drug design. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 167.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.2 KB 10.2 KB | Display Display | ![]() |
Images | ![]() | 48 KB | ||
Filedesc metadata | ![]() | 5.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 558 KB | Display | ![]() |
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Full document | ![]() | 557.6 KB | Display | |
Data in XML | ![]() | 7.1 KB | Display | |
Data in CIF | ![]() | 8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7e27MC ![]() 7e26C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 0.6746 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : PfFNT
Entire | Name: PfFNT |
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Components |
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-Supramolecule #1: PfFNT
Supramolecule | Name: PfFNT / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Formate-nitrite transporter
Macromolecule | Name: Formate-nitrite transporter / type: protein_or_peptide / ID: 1 / Details: MMV007839 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 34.492281 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MPPNNSKYVL DPVSIKSVCG GEESYIRCVE YGKKKAHYSN LNLLAKAILA GMFVGLCAHA SGIAGGLFYY HKLREIVGAS MSVFVYGFT FPIAFMCIIC TGSDLFTGNT LAVTMALYEK KVKLLDYLRV MTISLFGNYV GAVSFAFFVS YLSGAFTNVH A VEKNHFFQ ...String: MPPNNSKYVL DPVSIKSVCG GEESYIRCVE YGKKKAHYSN LNLLAKAILA GMFVGLCAHA SGIAGGLFYY HKLREIVGAS MSVFVYGFT FPIAFMCIIC TGSDLFTGNT LAVTMALYEK KVKLLDYLRV MTISLFGNYV GAVSFAFFVS YLSGAFTNVH A VEKNHFFQ FLNDIAEKKV HHTFVECVSL AVGCNIFVCL AVYFVLTLKD GAGYVFSVFF AVYAFAIAGY EHIIANIYTL NI ALMVNTK ITVYQAYIKN LLPTLLGNYI AGAIVLGLPL YFIYKEHYYN FERSKRDNND AQMKSLSIEL RN UniProtKB: Formate-nitrite transporter |
-Macromolecule #2: (Z)-4,4,5,5,5-pentakis(fluoranyl)-1-(4-methoxy-2-oxidanyl-phenyl)...
Macromolecule | Name: (Z)-4,4,5,5,5-pentakis(fluoranyl)-1-(4-methoxy-2-oxidanyl-phenyl)-3-oxidanyl-pent-2-en-1-one type: ligand / ID: 2 / Number of copies: 5 / Formula: HV6 |
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Molecular weight | Theoretical: 312.189 Da |
Chemical component information | ![]() ChemComp-HV6: |
-Macromolecule #3: water
Macromolecule | Name: water / type: ligand / ID: 3 / Number of copies: 90 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ![]() ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.29 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 291994 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |