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Yorodumi- EMDB-11726: Sub-nanometer cryo-EM density map of the human heterodimeric amin... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11726 | |||||||||
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Title | Sub-nanometer cryo-EM density map of the human heterodimeric amino acid transporter 4F2hc-LAT2 | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.5 Å | |||||||||
Authors | Jeckelmann J-M / Fotiadis D | |||||||||
Funding support | Switzerland, 1 items
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Citation | Journal: Int J Mol Sci / Year: 2020 Title: Sub-Nanometer Cryo-EM Density Map of the Human Heterodimeric Amino Acid Transporter 4F2hc-LAT2. Authors: Jean-Marc Jeckelmann / Dimitrios Fotiadis / 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 ...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 , 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. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11726.map.gz | 11 MB | EMDB map data format | |
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Header (meta data) | emd-11726-v30.xml emd-11726.xml | 11.6 KB 11.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11726_fsc.xml | 8.4 KB | Display | FSC data file |
Images | emd_11726.png | 71.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11726 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11726 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_11726.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.66 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : 4F2hc-LAT2
Entire | Name: 4F2hc-LAT2 |
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Components |
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-Supramolecule #1: 4F2hc-LAT2
Supramolecule | Name: 4F2hc-LAT2 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all Details: heavy and light chain of the contently linked heterodimeric amino acid transporter |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 120 KDa |
Recombinant expression | Organism: Komagataella phaffii CBS 7435 (fungus) |
-Macromolecule #1: hLAT2
Macromolecule | Name: hLAT2 / type: protein_or_peptide / ID: 1 Details: light chain of the contently linked heterodimeric amino acid transporter Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Komagataella pastoris (fungus) |
Sequence | String: TMAWSHPQFE KIEGRMEEGA RHRNNTEKKH PGGGESDASP EAGSGGGGVA LKKEIGLVSA CGIIVGNIIG SGIFVSPKGV LENAGSVGLA LIVWIVTGFI TVVGALCYAE LGVTIPKSGG DYSYVKDIFG GLAGFLRLWI AVLVIYPTNQ AVIALTFSNY VLQPLFPTCF ...String: TMAWSHPQFE KIEGRMEEGA RHRNNTEKKH PGGGESDASP EAGSGGGGVA LKKEIGLVSA CGIIVGNIIG SGIFVSPKGV LENAGSVGLA LIVWIVTGFI TVVGALCYAE LGVTIPKSGG DYSYVKDIFG GLAGFLRLWI AVLVIYPTNQ AVIALTFSNY VLQPLFPTCF PPESGLRLLA AICLLLLTWV NCSSVRWATR VQDIFTAGKL LALALIIIMG IVQICKGEYF WLEPKNAFEN FQEPDIGLVA LAFLQGSFAY GGWNFLNYVT EELVDPYKNL PRAIFISIPL VTFVYVFANV AYVTAMSPQE LLASNAVAVT FGEKLLGVMA WIMPISVALS TFGGVNGSLF TSSRLFFAGA REGHLPSVLA MIHVKRCTPI PALLFTCIST LLMLVTSDMY TLINYVGFIN YLFYGVTVAG QIVLRWKKPD IPRPIKINLL FPIIYLLFWA FLLVFSLWSE PVVCGIGLAI MLTGVPVYFL GVYWQHKPKC FSDFIELLTL VSQKMCVVVY PEVERGSGTE EANEDMEEQQ QPMYQPTPTK DKDVAGQPQP |
-Macromolecule #2: h4F2hc
Macromolecule | Name: h4F2hc / type: protein_or_peptide / ID: 2 Details: heavy chain of the contently linked heterodimeric amino acid transporter Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Komagataella phaffii CBS 7435 (fungus) |
Sequence | String: TMAHHHHHHH HHGIEGRMSQ DTEVDMKEVE LNELEPEKQP MNAASGAAMS LAGAEKNGLV KIKVAEDEAE AAAAAKFTGL SKEELLKVAG SPGWVRTRWA LLLLFWLGWL GMLAGAVVII VRAPRCRELP AQKWWHTGAL YRIGDLQAFQ GHGAGNLAGL KGRLDYLSSL ...String: TMAHHHHHHH HHGIEGRMSQ DTEVDMKEVE LNELEPEKQP MNAASGAAMS LAGAEKNGLV KIKVAEDEAE AAAAAKFTGL SKEELLKVAG SPGWVRTRWA LLLLFWLGWL GMLAGAVVII VRAPRCRELP AQKWWHTGAL YRIGDLQAFQ GHGAGNLAGL KGRLDYLSSL KVKGLVLGPI HKNQKDDVAQ TDLLQIDPNF GSKEDFDSLL QSAKKKSIRV ILDLTPNYRG ENSWFSTQVD TVATKVKDAL EFWLQAGVDG FQVRDIENLK DASSFLAEWQ NITKGFSEDR LLIAGTNSSD LQQILSLLES NKDLLLTSSY LSDSGSTGEH TKSLVTQYLN ATGNRWCSWS LSQARLLTSF LPAQLLRLYQ LMLFTLPGTP VFSYGDEIGL DAAALPGQPM EAPVMLWDES SFPDIPGAVS ANMTVKGQSE DPGSLLSLFR RLSDQRSKER SLLHGDFHAF SAGPGLFSYI RHWDQNERFL VVLNFGDVGL SAGLQASDLP ASASLPAKAD LLLSTQPGRE EGSPLELERL KLEPHEGLLL RFPYAA |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3 mg/mL |
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Buffer | pH: 6.8 |
Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 101.325 kPa |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |