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Yorodumi- EMDB-15393: Cryo-EM structure of a substrate-bound glutamate transporter homo... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15393 | |||||||||
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Title | Cryo-EM structure of a substrate-bound glutamate transporter homologue GltTk encapsulated within a nanodisc | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Glutamate / transporter / mutant / nanodisc / TRANSPORT PROTEIN | |||||||||
Function / homology | carboxylic acid transport / Sodium:dicarboxylate symporter / Sodium:dicarboxylate symporter, conserved site / Sodium:dicarboxylate symporter superfamily / Sodium:dicarboxylate symporter family / Sodium:dicarboxylate symporter family signature 1. / symporter activity / membrane / Proton/glutamate symporter, SDF family Function and homology information | |||||||||
Biological species | Thermococcus kodakarensis (archaea) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.25 Å | |||||||||
Authors | Whittaker JJ / Guskov A | |||||||||
Funding support | Netherlands, 1 items
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Citation | Journal: Nat Commun / Year: 2020 Title: Structural ensemble of a glutamate transporter homologue in lipid nanodisc environment. Authors: Valentina Arkhipova / Albert Guskov / Dirk J Slotboom / Abstract: Glutamate transporters are cation-coupled secondary active membrane transporters that clear the neurotransmitter L-glutamate from the synaptic cleft. These transporters are homotrimers, with each ...Glutamate transporters are cation-coupled secondary active membrane transporters that clear the neurotransmitter L-glutamate from the synaptic cleft. These transporters are homotrimers, with each protomer functioning independently by an elevator-type mechanism, in which a mobile transport domain alternates between inward- and outward-oriented states. Using single-particle cryo-EM we have determined five structures of the glutamate transporter homologue Glt, a Na- L-aspartate symporter, embedded in lipid nanodiscs. Dependent on the substrate concentrations used, the protomers of the trimer adopt a variety of asymmetrical conformations, consistent with the independent movement. Six of the 15 resolved protomers are in a hitherto elusive state of the transport cycle in which the inward-facing transporters are loaded with Na ions. These structures explain how substrate-leakage is prevented - a strict requirement for coupled transport. The belt protein of the lipid nanodiscs bends around the inward oriented protomers, suggesting that membrane deformations occur during transport. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15393.map.gz | 59.5 MB | EMDB map data format | |
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Header (meta data) | emd-15393-v30.xml emd-15393.xml | 16.9 KB 16.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15393_fsc.xml | 11.8 KB | Display | FSC data file |
Images | emd_15393.png | 123.9 KB | ||
Filedesc metadata | emd-15393.cif.gz | 6.1 KB | ||
Others | emd_15393_half_map_1.map.gz emd_15393_half_map_2.map.gz | 58.7 MB 58.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15393 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15393 | HTTPS FTP |
-Validation report
Summary document | emd_15393_validation.pdf.gz | 752.5 KB | Display | EMDB validaton report |
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Full document | emd_15393_full_validation.pdf.gz | 752.1 KB | Display | |
Data in XML | emd_15393_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | emd_15393_validation.cif.gz | 21.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15393 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15393 | HTTPS FTP |
-Related structure data
Related structure data | 8afaMC 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_15393.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.836 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_15393_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_15393_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Glutamate transporter homologue GltTK in a lipid nanodisc environ...
Entire | Name: Glutamate transporter homologue GltTK in a lipid nanodisc environment bound with L-aspartate ligands |
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Components |
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-Supramolecule #1: Glutamate transporter homologue GltTK in a lipid nanodisc environ...
Supramolecule | Name: Glutamate transporter homologue GltTK in a lipid nanodisc environment bound with L-aspartate ligands type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Thermococcus kodakarensis (archaea) / Strain: BL21(DE3) |
Molecular weight | Theoretical: 1.39 MDa |
-Macromolecule #1: Proton/glutamate symporter, SDF family
Macromolecule | Name: Proton/glutamate symporter, SDF family / type: protein_or_peptide / ID: 1 / Details: Mutant P208R / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Thermococcus kodakarensis (archaea) / Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Cell: E.coli |
Molecular weight | Theoretical: 46.745441 KDa |
Recombinant expression | Organism: Thermococcus kodakarensis (archaea) |
Sequence | String: MGKSLLRRYL DYPVLWKILW GLVLGAVFGL IAGHFGYAGA VKTYIKPFGD LFVRLLKMLV MPIVLASLVV GAASISPARL GRVGVKIVV YYLATSAMAV FFGLIVGRLF NVGANVNLGS GTGKAIEAQP PSLVQTLLNI VPTNPFASLA KGEVLPVIFF A IILGIAIT ...String: MGKSLLRRYL DYPVLWKILW GLVLGAVFGL IAGHFGYAGA VKTYIKPFGD LFVRLLKMLV MPIVLASLVV GAASISPARL GRVGVKIVV YYLATSAMAV FFGLIVGRLF NVGANVNLGS GTGKAIEAQP PSLVQTLLNI VPTNPFASLA KGEVLPVIFF A IILGIAIT YLMNRNEERV RKSAETLLRV FDGLAEAMYL IVGGVMQYAR IGVFALIAYV MAEQGVRVVG PLAKVVGAVY TG LFLQIVI TYFILLKVFG IDPIKFIRKA KDAMITAFVT RSSSGTLPVT MRVAEEEMGV DKGIFSFTLP LGATINMDGT ALY QGVTVL FVANAIGHPL TLGQQLVVVL TAVLASIGTA GVPGAGAIML AMVLQSVGLD LTPGSPVALA YAMILGIDAI LDMG RTMVN VTGDLAGTVI VAKTEKELDE SKWISHHHHH HHH UniProtKB: Proton/glutamate symporter, SDF family |
-Macromolecule #2: ASPARTIC ACID
Macromolecule | Name: ASPARTIC ACID / type: ligand / ID: 2 / Number of copies: 3 / Formula: ASP |
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Molecular weight | Theoretical: 133.103 Da |
Chemical component information | ChemComp-ASP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.5 mg/mL | ||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 100 | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Digitization - Scanner: OTHER / Average electron dose: 50.0 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: 5.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |