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Yorodumi- EMDB-26997: Human excitatory amino acid transporter 3 (EAAT3) with bound pota... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26997 | |||||||||
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Title | Human excitatory amino acid transporter 3 (EAAT3) with bound potassium in an intermediate outward facing state | |||||||||
Map data | human Excitatory amino acid transporter 3 with potassium bound at intermediate outward facing (iOFS)state | |||||||||
Sample |
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Function / homology | Function and homology information D-aspartate transmembrane transport / response to anesthetic / regulation of protein targeting to membrane / D-aspartate transmembrane transporter activity / Defective SLC1A1 is implicated in schizophrenia 18 (SCZD18) and dicarboxylic aminoaciduria (DCBXA) / response to decreased oxygen levels / distal dendrite / cysteine transmembrane transporter activity / cysteine transport / high-affinity L-glutamate transmembrane transporter activity ...D-aspartate transmembrane transport / response to anesthetic / regulation of protein targeting to membrane / D-aspartate transmembrane transporter activity / Defective SLC1A1 is implicated in schizophrenia 18 (SCZD18) and dicarboxylic aminoaciduria (DCBXA) / response to decreased oxygen levels / distal dendrite / cysteine transmembrane transporter activity / cysteine transport / high-affinity L-glutamate transmembrane transporter activity / glutamate:sodium symporter activity / L-glutamate import / neurotransmitter receptor transport to plasma membrane / cellular response to mercury ion / Transport of inorganic cations/anions and amino acids/oligopeptides / zinc ion transmembrane transport / retina layer formation / L-glutamate transmembrane transport / L-glutamate transmembrane transporter activity / cellular response to bisphenol A / L-aspartate transmembrane transport / D-aspartate import across plasma membrane / cellular response to ammonium ion / proximal dendrite / glutathione biosynthetic process / righting reflex / monoatomic anion channel activity / grooming behavior / L-aspartate transmembrane transporter activity / intracellular glutamate homeostasis / L-aspartate import across plasma membrane / Glutamate Neurotransmitter Release Cycle / L-glutamate import across plasma membrane / conditioned place preference / transepithelial transport / apical dendrite / intracellular zinc ion homeostasis / glutamate receptor signaling pathway / response to morphine / neurotransmitter transport / cellular response to cocaine / blood vessel morphogenesis / motor behavior / motor neuron apoptotic process / chloride transmembrane transporter activity / glutamate binding / G protein-coupled dopamine receptor signaling pathway / positive regulation of heart rate / adult behavior / postsynaptic modulation of chemical synaptic transmission / dopamine metabolic process / maintenance of blood-brain barrier / heart contraction / superoxide metabolic process / perisynaptic space / glial cell projection / cellular response to organic cyclic compound / transport across blood-brain barrier / asymmetric synapse / response to axon injury / behavioral fear response / neurogenesis / monoatomic ion transport / synaptic cleft / axon terminus / chloride transmembrane transport / response to amphetamine / dendritic shaft / locomotory behavior / cell periphery / long-term synaptic potentiation / synapse organization / regulation of protein phosphorylation / brain development / Schaffer collateral - CA1 synapse / memory / cytokine-mediated signaling pathway / recycling endosome membrane / early endosome membrane / late endosome membrane / presynapse / gene expression / cellular response to oxidative stress / chemical synaptic transmission / perikaryon / negative regulation of neuron apoptotic process / dendritic spine / apical plasma membrane / response to xenobiotic stimulus / membrane raft / axon / neuronal cell body / dendrite / cell surface / endoplasmic reticulum / extracellular exosome / identical protein binding / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.44 Å | |||||||||
Authors | Qiu B / Boudker O | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Symport and antiport mechanisms of human glutamate transporters. Authors: Biao Qiu / Olga Boudker / Abstract: Excitatory amino acid transporters (EAATs) uptake glutamate into glial cells and neurons. EAATs achieve million-fold transmitter gradients by symporting it with three sodium ions and a proton, and ...Excitatory amino acid transporters (EAATs) uptake glutamate into glial cells and neurons. EAATs achieve million-fold transmitter gradients by symporting it with three sodium ions and a proton, and countertransporting a potassium ion via an elevator mechanism. Despite the availability of structures, the symport and antiport mechanisms still need to be clarified. We report high-resolution cryo-EM structures of human EAAT3 bound to the neurotransmitter glutamate with symported ions, potassium ions, sodium ions alone, or without ligands. We show that an evolutionarily conserved occluded translocation intermediate has a dramatically higher affinity for the neurotransmitter and the countertransported potassium ion than outward- or inward-facing transporters and plays a crucial role in ion coupling. We propose a comprehensive ion coupling mechanism involving a choreographed interplay between bound solutes, conformations of conserved amino acid motifs, and movements of the gating hairpin and the substrate-binding domain. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26997.map.gz | 97 MB | EMDB map data format | |
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Header (meta data) | emd-26997-v30.xml emd-26997.xml | 18.4 KB 18.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_26997_fsc.xml | 10.4 KB | Display | FSC data file |
Images | emd_26997.png | 56.9 KB | ||
Others | emd_26997_half_map_1.map.gz emd_26997_half_map_2.map.gz | 95.5 MB 95.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26997 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26997 | HTTPS FTP |
-Validation report
Summary document | emd_26997_validation.pdf.gz | 818.8 KB | Display | EMDB validaton report |
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Full document | emd_26997_full_validation.pdf.gz | 818.3 KB | Display | |
Data in XML | emd_26997_validation.xml.gz | 18.3 KB | Display | |
Data in CIF | emd_26997_validation.cif.gz | 23.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26997 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26997 | HTTPS FTP |
-Related structure data
Related structure data | 8cuaMC 8ctcC 8ctdC 8cudC 8cuiC 8cujC 8cv2C 8cv3C 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_26997.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | human Excitatory amino acid transporter 3 with potassium bound at intermediate outward facing (iOFS)state | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.852 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half Map 1
File | emd_26997_half_map_1.map | ||||||||||||
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Annotation | Half Map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half Map 2
File | emd_26997_half_map_2.map | ||||||||||||
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Annotation | Half Map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Human EAAT3 with potassium bound
Entire | Name: Human EAAT3 with potassium bound |
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Components |
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-Supramolecule #1: Human EAAT3 with potassium bound
Supramolecule | Name: Human EAAT3 with potassium bound / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #2: Human EAAT3 with potassium bound
Supramolecule | Name: Human EAAT3 with potassium bound / type: complex / ID: 2 / Chimera: Yes / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Excitatory amino acid transporter 3
Macromolecule | Name: Excitatory amino acid transporter 3 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 57.120863 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: GPMGKPARKG AEWKRFLKNN WVLLSTVAAV VLGITTGVLV REHSNLSTLE KFYFAFPGEI LMRMLKLIIL PLIISSMITG VAALDSNVS GKIGLRAVVY YFATTLIAVI LGIVLVVSIK PGVTQKVGEI ARTGSTPEVS TVDAMLDLIR NMFPENLVQA A FQQYKTKR ...String: GPMGKPARKG AEWKRFLKNN WVLLSTVAAV VLGITTGVLV REHSNLSTLE KFYFAFPGEI LMRMLKLIIL PLIISSMITG VAALDSNVS GKIGLRAVVY YFATTLIAVI LGIVLVVSIK PGVTQKVGEI ARTGSTPEVS TVDAMLDLIR NMFPENLVQA A FQQYKTKR EEVKPPSDPE MTMTEESFTA VMTTAISKTK TKEYKIVGMY SDGINVLGLI VFALVFGLVI GKMGEKGQIL VD FFNALSD ATMKIVQIIM WYMPLGILFL IAGCIIEVED WEIFRKLGLY MATVLTGLAI HSIVILPLIY FIVVRKNPFR FAM GMAQAL LTALMISSSS ATLPVTFRCA EENNQVDKRI TRFVLPVGAT INMDGTALYE AVAAVFIAQL NDLDLGIGQI ITIS ITATS ASIGAAGVPQ AGLVTMVIVL SAVGLPAEDV TLIIAVDCLL DRFRTMVNVL GDAFGTGIVE KLSKKELEQM DVSSE VNIV NPFALESTIL DNEDSDTKKS YVNGGFAVDK SDTISFTQTS QF |
-Macromolecule #2: POTASSIUM ION
Macromolecule | Name: POTASSIUM ION / type: ligand / ID: 2 / Number of copies: 3 / Formula: K |
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Molecular weight | Theoretical: 39.098 Da |
-Macromolecule #3: MERCURY (II) ION
Macromolecule | Name: MERCURY (II) ION / type: ligand / ID: 3 / Number of copies: 3 / Formula: HG |
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Molecular weight | Theoretical: 200.59 Da |
-Macromolecule #4: water
Macromolecule | Name: water / type: ligand / ID: 4 / Number of copies: 30 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 6.2 mg/mL | ||||||||||||
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Buffer | pH: 7.4 Component:
Details: Tris is used fot adjusting pH | ||||||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot 3s. | ||||||||||||
Details | the sample was monodisperse |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 51.1 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.3 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |