+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22020 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | hEAAT3-Asymmetric-1o2i | |||||||||
Map data | Asymmetric, Outward-facing bound, Inward-facing open | |||||||||
Sample |
| |||||||||
Keywords | Asymmetric / Outward-facing bound / Inward-facing open / TRANSPORT PROTEIN | |||||||||
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: 3.42 Å | |||||||||
Authors | Qiu B / Matthies D | |||||||||
Funding support | United States, 1 items
| |||||||||
Citation | Journal: Sci Adv / Year: 2021 Title: Cryo-EM structures of excitatory amino acid transporter 3 visualize coupled substrate, sodium, and proton binding and transport. Authors: Biao Qiu / Doreen Matthies / Eva Fortea / Zhiheng Yu / Olga Boudker / Abstract: Human excitatory amino acid transporter 3 (hEAAT3) mediates glutamate uptake in neurons, intestine, and kidney. Here, we report cryo-EM structures of hEAAT3 in several functional states where the ...Human excitatory amino acid transporter 3 (hEAAT3) mediates glutamate uptake in neurons, intestine, and kidney. Here, we report cryo-EM structures of hEAAT3 in several functional states where the transporter is empty, bound to coupled sodium ions only, or fully loaded with three sodium ions, a proton, and the substrate aspartate. The structures suggest that hEAAT3 operates by an elevator mechanism involving three functionally independent subunits. When the substrate-binding site is near the cytoplasm, it has a remarkably low affinity for the substrate, perhaps facilitating its release and allowing the rapid transport turnover. The mechanism of the coupled uptake of the sodium ions and the substrate is conserved across evolutionarily distant families and is augmented by coupling to protons in EAATs. The structures further suggest a mechanism by which a conserved glutamate residue mediates proton symport. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_22020.map.gz | 85.2 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-22020-v30.xml emd-22020.xml | 13.6 KB 13.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_22020_fsc.xml | 10.3 KB | Display | FSC data file |
Images | emd_22020.png | 36.3 KB | ||
Filedesc metadata | emd-22020.cif.gz | 5.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22020 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22020 | HTTPS FTP |
-Validation report
Summary document | emd_22020_validation.pdf.gz | 582 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_22020_full_validation.pdf.gz | 581.6 KB | Display | |
Data in XML | emd_22020_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | emd_22020_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22020 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22020 | HTTPS FTP |
-Related structure data
Related structure data | 6x3eMC 6x2lC 6x2zC 6x3fC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_22020.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Asymmetric, Outward-facing bound, Inward-facing open | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.832 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Asymmetric hEAAT3 trimer
Entire | Name: Asymmetric hEAAT3 trimer |
---|---|
Components |
|
-Supramolecule #1: Asymmetric hEAAT3 trimer
Supramolecule | Name: Asymmetric hEAAT3 trimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
---|---|
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 Details: The Glycine and Proline at the N terminal are the residues left after PreScission Protease treatment Number of copies: 3 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 57.301168 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: GPMGKPARKG CEWKRFLKNN WVLLSTVAAV VLGITTGVLV REHSNLSTLE KFYFAFPGEI LMRMLKLIIL PLIISSMITG VAALDSNVS GKIGLRAVVY YFCTTLIAVI LGIVLVVSIK PGVTQKVGEI ARTGSTPEVS TVDAMLDLIR NMFPENLVQA C FQQYKTKR ...String: GPMGKPARKG CEWKRFLKNN WVLLSTVAAV VLGITTGVLV REHSNLSTLE KFYFAFPGEI LMRMLKLIIL PLIISSMITG VAALDSNVS GKIGLRAVVY YFCTTLIAVI LGIVLVVSIK PGVTQKVGEI ARTGSTPEVS TVDAMLDLIR NMFPENLVQA C FQQYKTKR EEVKPPSDPE MNMTEESFTA VMTTAISKNK TKEYKIVGMY SDGINVLGLI VFCLVFGLVI GKMGEKGQIL VD FFNALSD ATMKIVQIIM CYMPLGILFL IAGKIIEVED WEIFRKLGLY MATVLTGLAI HSIVILPLIY FIVVRKNPFR FAM GMAQAL LTALMISSSS ATLPVTFRCA EENNQVDKRI TRFVLPVGAT INMDGTALYE AVAAVFIAQL NDLDLGIGQI ITIS ITATS ASIGAAGVPQ AGLVTMVIVL SAVGLPAEDV TLIIAVDWLL DRFRTMVNVL GDAFGTGIVE KLSKKELEQM DVSSE VNIV NPFALESTIL DNEDSDTKKS YVNGGFAVDK SDTISFTQTS QF UniProtKB: Excitatory amino acid transporter 3 |
-Macromolecule #2: ASPARTIC ACID
Macromolecule | Name: ASPARTIC ACID / type: ligand / ID: 2 / Number of copies: 1 / Formula: ASP |
---|---|
Molecular weight | Theoretical: 133.103 Da |
Chemical component information | ChemComp-ASP: |
-Macromolecule #3: SODIUM ION
Macromolecule | Name: SODIUM ION / type: ligand / ID: 3 / Number of copies: 3 |
---|---|
Molecular weight | Theoretical: 22.99 Da |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 6 mg/mL | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 8 Component:
| ||||||||||||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / 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 | This sample was mono disperse |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 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 / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 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 |