Dataset Information

Sub-Nanometer Cryo-EM Density Map of the Human Heterodimeric Amino Acid Transporter 4F2hc-LAT2.

ABSTRACT: Heterodimeric amino acid transporters (HATs) are protein complexes mediating the transport of amino acids and derivatives thereof across biological membranes. HATs are composed of two subunits, a heavy and a light chain subunit belonging to the solute carrier (SLC) families SLC3 and SLC7. The human HAT 4F2hc-LAT2 is composed of the type-II membrane N-glycoprotein 4F2hc (SCL3A2) and the L-type amino acid transporter LAT2 (SLC7A8), which are covalently linked to each other by a conserved disulfide bridge. Whereas LAT2 catalyzes substrate transport, 4F2hc is important for the successful trafficking of the transporter to the plasma membrane. The overexpression, malfunction, or absence of 4F2hc-LAT2 is associated with human diseases, and therefore, this heterodimeric complex represents a potential drug target. The recombinant human 4F2hc-LAT2 can be functionally overexpressed in the methylotrophic yeast Pichia pastoris, and the protein can be purified. Here, we present the cryo-EM density map of the human 4F2hc-LAT2 amino acid transporter at sub-nanometer resolution. A homology model of 4F2hc-LAT2 in the inward-open conformation was generated and fitted into the cryo-EM density and analyzed. In addition, disease-causing point mutations in human LAT2 were mapped on the homology model of 4F2hc-LAT2, and the possible functional implications on the molecular level are discussed.

SUBMITTER: Jeckelmann JM

PROVIDER: S-EPMC7584034 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature

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Sub-Nanometer Cryo-EM Density Map of the Human Heterodimeric Amino Acid Transporter 4F2hc-LAT2.

Jeckelmann Jean-Marc JM Fotiadis Dimitrios D

International journal of molecular sciences 20200925 19

Heterodimeric amino acid transporters (HATs) are protein complexes mediating the transport of amino acids and derivatives thereof across biological membranes. HATs are composed of two subunits, a heavy and a light chain subunit belonging to the solute carrier (SLC) families SLC3 and SLC7. The human HAT 4F2hc-LAT2 is composed of the type-II membrane N-glycoprotein 4F2hc (SCL3A2) and the L-type amino acid transporter LAT2 (SLC7A8), which are covalently linked to each other by a conserved disulfide ...[more]

PMID: 32993041

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Project description:The cationic amino acid arginine, due to its positive charge, is usually accumulated in the cytosol. Nevertheless, arginine has to be released by a number of cell types, e.g. kidney cells, which supply other organs with this amino acid, or the endothelial cells of the blood-brain barrier which release arginine into the brain. Arginine release in mammalian cells can be mediated by two different transporters, y(+)LAT1 and y(+)LAT2. For insertion into the plasma membrane, these transporters have to be associated with the type-II membrane glycoprotein 4F2hc [Torrents, Estevez, Pineda, Fernandez, Lloberas, Shi, Zorzano and Palacin (1998) J. Biol. Chem. 273, 32437-32445]. The present study elucidates the function and distribution of y(+)LAT2. In contrast to y(+)LAT1, which is expressed mainly in kidney epithelial cells, lung and leucocytes, y(+)LAT2 has a wider tissue distribution, including brain, heart, testis, kidney, small intestine and parotis. When co-expressed with 4F2hc in Xenopus laevis oocytes, y(+)LAT2 mediated uptake of arginine, leucine and glutamine. Arginine uptake was inhibited strongly by lysine, glutamate, leucine, glutamine, methionine and histidine. Mutual inhibition was observed when leucine or glutamine was used as substrate. Inhibition of arginine uptake by neutral amino acids depended on the presence of Na(+), which is a hallmark of y(+)LAT-type transporters. Although arginine transport was inhibited strongly by glutamate, this anionic amino acid was only weakly transported by 4F2hc/y(+)LAT2. Amino acid transport via 4F2hc/y(+)LAT2 followed an antiport mechanism similar to the other members of this new family. Only preloaded arginine could be released in exchange for extracellular amino acids, whereas marginal release of glutamine or leucine was observed under identical conditions. These results indicated that arginine has the highest affinity for the intracellular binding site and that arginine release may be the main physiological function of this transporter.

Project description:BackgroundCryo-EM data generated by electron tomography (ET) contains images for individual protein particles in different orientations and tilted angles. Individual cryo-EM particles can be aligned to reconstruct a 3D density map of a protein structure. However, low contrast and high noise in particle images make it challenging to build 3D density maps at intermediate to high resolution (1-3 Å). To overcome this problem, we propose a fully automated cryo-EM 3D density map reconstruction approach based on deep learning particle picking.ResultsA perfect 2D particle mask is fully automatically generated for every single particle. Then, it uses a computer vision image alignment algorithm (image registration) to fully automatically align the particle masks. It calculates the difference of the particle image orientation angles to align the original particle image. Finally, it reconstructs a localized 3D density map between every two single-particle images that have the largest number of corresponding features. The localized 3D density maps are then averaged to reconstruct a final 3D density map. The constructed 3D density map results illustrate the potential to determine the structures of the molecules using a few samples of good particles. Also, using the localized particle samples (with no background) to generate the localized 3D density maps can improve the process of the resolution evaluation in experimental maps of cryo-EM. Tested on two widely used datasets, Auto3DCryoMap is able to reconstruct good 3D density maps using only a few thousand protein particle images, which is much smaller than hundreds of thousands of particles required by the existing methods.ConclusionsWe design a fully automated approach for cryo-EM 3D density maps reconstruction (Auto3DCryoMap). Instead of increasing the signal-to-noise ratio by using 2D class averaging, our approach uses 2D particle masks to produce locally aligned particle images. Auto3DCryoMap is able to accurately align structural particle shapes. Also, it is able to construct a decent 3D density map from only a few thousand aligned particle images while the existing tools require hundreds of thousands of particle images. Finally, by using the pre-processed particle images, Auto3DCryoMap reconstructs a better 3D density map than using the original particle images.

Dataset Information

Sub-Nanometer Cryo-EM Density Map of the Human Heterodimeric Amino Acid Transporter 4F2hc-LAT2.

Publications

Sub-Nanometer Cryo-EM Density Map of the Human Heterodimeric Amino Acid Transporter 4F2hc-LAT2.

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