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Yorodumi- PDB-8ctc: Human excitatory amino acid transporter 3 (EAAT3) with bound glut... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ctc | ||||||
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Title | Human excitatory amino acid transporter 3 (EAAT3) with bound glutamate in an intermediate outward facing state | ||||||
Components | Excitatory amino acid transporter 3 | ||||||
Keywords | TRANSPORT PROTEIN | ||||||
Function / homology | Function and homology information D-aspartate transmembrane transport / 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 / response to anesthetic / cysteine transmembrane transporter activity / cysteine transport / neurotransmitter receptor transport to plasma membrane ...D-aspartate transmembrane transport / 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 / response to anesthetic / cysteine transmembrane transporter activity / cysteine transport / neurotransmitter receptor transport to plasma membrane / high-affinity L-glutamate transmembrane transporter activity / glutamate:sodium symporter activity / L-glutamate import / 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 / glutathione biosynthetic process / cellular response to ammonium ion / D-aspartate import across plasma membrane / righting reflex / apical dendrite / monoatomic anion channel activity / L-aspartate transmembrane transporter activity / intracellular glutamate homeostasis / L-aspartate import across plasma membrane / grooming behavior / Glutamate Neurotransmitter Release Cycle / proximal dendrite / L-glutamate import across plasma membrane / transepithelial transport / conditioned place preference / intracellular zinc ion homeostasis / cellular response to cocaine / blood vessel morphogenesis / neurotransmitter transport / motor behavior / response to morphine / motor neuron apoptotic process / chloride transmembrane transporter activity / glutamate receptor signaling pathway / glutamate binding / positive regulation of heart rate / G protein-coupled dopamine receptor signaling pathway / adult behavior / postsynaptic modulation of chemical synaptic transmission / maintenance of blood-brain barrier / heart contraction / superoxide metabolic process / dopamine metabolic process / perisynaptic space / cellular response to organic cyclic compound / transport across blood-brain barrier / glial cell projection / behavioral fear response / asymmetric synapse / response to axon injury / synaptic cleft / monoatomic ion transport / axon terminus / chloride transmembrane transport / response to amphetamine / neurogenesis / dendritic shaft / cell periphery / locomotory behavior / long-term synaptic potentiation / brain development / regulation of protein phosphorylation / synapse organization / Schaffer collateral - CA1 synapse / cytokine-mediated signaling pathway / memory / recycling endosome membrane / late endosome membrane / presynapse / cellular response to oxidative stress / gene expression / early endosome membrane / chemical synaptic transmission / perikaryon / negative regulation of neuron apoptotic process / dendritic spine / response to xenobiotic stimulus / apical plasma membrane / 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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||
Authors | Qiu, B. / Boudker, O. | ||||||
Funding support | United States, 1items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ctc.cif.gz | 237.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ctc.ent.gz | 188.7 KB | Display | PDB format |
PDBx/mmJSON format | 8ctc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ctc_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8ctc_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8ctc_validation.xml.gz | 45.7 KB | Display | |
Data in CIF | 8ctc_validation.cif.gz | 68.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ct/8ctc ftp://data.pdbj.org/pub/pdb/validation_reports/ct/8ctc | HTTPS FTP |
-Related structure data
Related structure data | 26985MC 8ctdC 8cuaC 8cudC 8cuiC 8cujC 8cv2C 8cv3C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 57120.863 Da / Num. of mol.: 3 Mutation: C9A, C100A, C158A, N178T, N195T, C219A, C256W, K269C, W441C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SLC1A1, EAAC1, EAAT3 / Production host: Homo sapiens (human) / References: UniProt: P43005 #2: Chemical | #3: Chemical | ChemComp-NA / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.4 / Details: Tris is used for adjusting pH | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 4.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Human EAAT3 with glutamate bound | |||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: blot 3s |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm / C2 aperture diameter: 100 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50.266 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: UCSF ChimeraX / Version: 1.2/v9 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: macOS / Type: package | ||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 8511485 | ||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C3 (3 fold cyclic) | ||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 496972 / Symmetry type: POINT | ||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | ||||||||||||||||||||||||||||||
Atomic model building |
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