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- EMDB-30952: Structure of PfFNT in apo state -

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Basic information

Entry
Database: EMDB / ID: EMD-30952
TitleStructure of PfFNT in apo state
Map data
Sample
  • Complex: Pentameric complex of FNT
    • Protein or peptide: Formate-nitrite transporter
  • Ligand: water
KeywordsLactate / transporter / TRANSPORT PROTEIN
Function / homology
Function and homology information


high-affinity secondary active nitrite transmembrane transporter activity / lactate transmembrane transport / nitrite transport / lactate:proton symporter activity / plasma membrane
Similarity search - Function
Formate and nitrite transporters signature 2. / Formate/nitrite transporter / Formate/nitrite transporter, conserved site / Formate/nitrite transporter / Aquaporin-like
Similarity search - Domain/homology
Formate-nitrite transporter
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.29 Å
AuthorsYan CY / Jiang X / Peng X / Wang N / Zhu A / Xu H / Li J
CitationJournal: PLoS Biol / Year: 2021
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
DepositionFeb 4, 2021-
Header (metadata) releaseAug 18, 2021-
Map releaseAug 18, 2021-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7e26
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30952.png

Downloads & links

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Map

FileDownload / File: emd_30952.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.67 Å/pix.
x 360 pix.
= 242.856 Å		0.67 Å/pix.
x 360 pix.
= 242.856 Å		0.67 Å/pix.
x 360 pix.
= 242.856 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.6746 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5 / Movie #1: 0.5
Minimum - Maximum-1.3622991 - 2.1964474
Average (Standard dev.)0.006371587 (±0.066059254)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 242.856 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.67460.67460.6746
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z242.856242.856242.856
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ500500500
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-1.3622.1960.006

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Supplemental data

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Sample components

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Entire : Pentameric complex of FNT

EntireName: Pentameric complex of FNT
Components
  • Complex: Pentameric complex of FNT
    • Protein or peptide: Formate-nitrite transporter
  • Ligand: water

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Supramolecule #1: Pentameric complex of FNT

SupramoleculeName: Pentameric complex of FNT / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)
Molecular weightTheoretical: 170 KDa

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Macromolecule #1: Formate-nitrite transporter

MacromoleculeName: Formate-nitrite transporter / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote) / Strain: 3D7
Molecular weightTheoretical: 34.492281 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 80 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.29 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 221350
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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