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- EMDB-12524: Cryo-EM structure of Human excitatory amino acid transporters-1 (... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-12524 | |||||||||
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Title | Cryo-EM structure of Human excitatory amino acid transporters-1 (EAAT1) in potassium buffer | |||||||||
![]() | Cryo-EM map of Human excitatory amino acid transporters (EAATs) | |||||||||
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![]() | Human Membrane Protein / Transporter / Glutamate transporter / MEMBRANE PROTEIN | |||||||||
Function / homology | ![]() Defective SLC1A3 causes episodic ataxia 6 (EA6) / auditory behavior / Astrocytic Glutamate-Glutamine Uptake And Metabolism / membrane protein complex / neurotransmitter uptake / cranial nerve development / cell morphogenesis involved in neuron differentiation / gamma-aminobutyric acid biosynthetic process / high-affinity L-glutamate transmembrane transporter activity / glutamate:sodium symporter activity ...Defective SLC1A3 causes episodic ataxia 6 (EA6) / auditory behavior / Astrocytic Glutamate-Glutamine Uptake And Metabolism / membrane protein complex / neurotransmitter uptake / cranial nerve development / cell morphogenesis involved in neuron differentiation / gamma-aminobutyric acid biosynthetic process / high-affinity L-glutamate transmembrane transporter activity / glutamate:sodium symporter activity / L-glutamate import / Transport of inorganic cations/anions and amino acids/oligopeptides / L-glutamate transmembrane transport / L-glutamate transmembrane transporter activity / D-aspartate import across plasma membrane / L-aspartate import across plasma membrane / neutral L-amino acid transmembrane transporter activity / Glutamate Neurotransmitter Release Cycle / L-glutamate import across plasma membrane / transepithelial transport / intracellular sodium ion homeostasis / neurotransmitter transport / cellular response to cocaine / glutamate binding / neuromuscular process controlling balance / transport across blood-brain barrier / response to light stimulus / positive regulation of synaptic transmission / monoatomic ion transport / potassium ion transmembrane transport / chloride transmembrane transport / basal plasma membrane / sensory perception of sound / response to wounding / cytoplasmic vesicle / chemical synaptic transmission / response to xenobiotic stimulus / neuron projection / response to antibiotic / neuronal cell body / synapse / perinuclear region of cytoplasm / cell surface / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.99 Å | |||||||||
![]() | Kumar A / Reyes N | |||||||||
Funding support | ![]()
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![]() | ![]() Title: The ion-coupling mechanism of human excitatory amino acid transporters. Authors: Juan C Canul-Tec / Anand Kumar / Jonathan Dhenin / Reda Assal / Pierre Legrand / Martial Rey / Julia Chamot-Rooke / Nicolas Reyes / ![]() Abstract: Excitatory amino acid transporters (EAATs) maintain glutamate gradients in the brain essential for neurotransmission and to prevent neuronal death. They use ionic gradients as energy source and co- ...Excitatory amino acid transporters (EAATs) maintain glutamate gradients in the brain essential for neurotransmission and to prevent neuronal death. They use ionic gradients as energy source and co-transport transmitter into the cytoplasm with Na and H , while counter-transporting K to re-initiate the transport cycle. However, the molecular mechanisms underlying ion-coupled transport remain incompletely understood. Here, we present 3D X-ray crystallographic and cryo-EM structures, as well as thermodynamic analysis of human EAAT1 in different ion bound conformations, including elusive counter-transport ion bound states. Binding energies of Na and H , and unexpectedly Ca , are coupled to neurotransmitter binding. Ca competes for a conserved Na site, suggesting a regulatory role for Ca in glutamate transport at the synapse, while H binds to a conserved glutamate residue stabilizing substrate occlusion. The counter-transported ion binding site overlaps with that of glutamate, revealing the K -based mechanism to exclude the transmitter during the transport cycle and to prevent its neurotoxic release on the extracellular side. | |||||||||
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 | ![]() | 230 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 14.3 KB 14.3 KB | Display Display | ![]() |
Images | ![]() | 133 KB | ||
Filedesc metadata | ![]() | 6.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 483.2 KB | Display | ![]() |
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Full document | ![]() | 482.8 KB | Display | |
Data in XML | ![]() | 7.2 KB | Display | |
Data in CIF | ![]() | 8.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7npwMC ![]() 7awlC ![]() 7awmC ![]() 7awnC ![]() 7awpC ![]() 7awqC 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
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM map of Human excitatory amino acid transporters (EAATs) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.814 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 : Human excitatory amino acid transporter 1
Entire | Name: Human excitatory amino acid transporter 1 |
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Components |
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-Supramolecule #1: Human excitatory amino acid transporter 1
Supramolecule | Name: Human excitatory amino acid transporter 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Excitatory amino acid transporter 1
Macromolecule | Name: Excitatory amino acid transporter 1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 51.078273 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: AKKKVQNITK EDVKSYLFRN AFVLLTVTAV IVGTILGFTL RPYRMSYREV KYFSFPGELL MRMLQMLVLP LIISSLVTGM AALDSKASG KMGMRAVVYY MTTTIIAVVI GIIIVIIIHP GKGTKENMHR EGKIVRVTAA DAFLDLIRNM FPPNLVEACF K QFKTNYEK ...String: AKKKVQNITK EDVKSYLFRN AFVLLTVTAV IVGTILGFTL RPYRMSYREV KYFSFPGELL MRMLQMLVLP LIISSLVTGM AALDSKASG KMGMRAVVYY MTTTIIAVVI GIIIVIIIHP GKGTKENMHR EGKIVRVTAA DAFLDLIRNM FPPNLVEACF K QFKTNYEK RSFKVPIQAN ETLVGAVINN VSEAMETLTR ITEELVPVPG SVNGVNALGL VVFSMCFGFV IGNMKEQGQA LR EFFDSLN EAIMRLVAVI MWYAPVGILF LIAGKIVEME DMGVIGGQLA MYTVTVIVGL LIHAVIVLPL LYFLVTRKNP WVF IGGLLQ ALITALGTSS SSATLPITFK CLEENNGVDK RVTRFVLPVG ATINMDGTAL YEALAAIFIA QVNNFELNFG QIIT ISITA TAASIGAAGI PQAGLVTMVI VLTSVGLPTD DITLIIAVDW FLDRLRTTTN VLGDSLGAGI VEHL UniProtKB: Excitatory amino acid transporter 1 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 4 mg/mL | ||||||||||||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: Grids were blotted for 4 Sec. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 13607 / Average electron dose: 42.3 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Details | For model building, the scaD and tranD of Rb+/Ba2+ bound X-ray structure were fitted into the EM map as separate rigid-bodies using Chimera. |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | ![]() PDB-7npw: |