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- EMDB-10094: Structure of human excitatory amino acid transporter 3 (EAAT3) in... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-10094 | |||||||||
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Title | Structure of human excitatory amino acid transporter 3 (EAAT3) in complex with TFB-TBOA | |||||||||
![]() | Post-processed RELION map used for building and refinement | |||||||||
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![]() | GLUTAMATE / ASPARTATE TRANSPORTER / CYSTEINE / INHIBITOR COMPLEX / MEMBRANE PROTEIN / Structural Genomics / Structural Genomics Consortium / SGC | |||||||||
Function / homology | ![]() 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 / monoatomic anion channel 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 / L-aspartate transmembrane transporter activity / L-aspartate import across plasma membrane / grooming behavior / intracellular glutamate homeostasis / 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 / glutamate binding / chloride transmembrane transporter activity / G protein-coupled dopamine receptor signaling pathway / adult behavior / positive regulation of heart rate / postsynaptic modulation of chemical synaptic transmission / maintenance of blood-brain barrier / dopamine metabolic process / superoxide metabolic process / heart contraction / 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 / monoatomic ion transport / synaptic cleft / axon terminus / chloride transmembrane transport / response to amphetamine / neurogenesis / dendritic shaft / locomotory behavior / cell periphery / long-term synaptic potentiation / synapse organization / regulation of protein phosphorylation / Schaffer collateral - CA1 synapse / brain development / memory / cytokine-mediated signaling pathway / recycling endosome membrane / presynapse / late endosome membrane / gene expression / cellular response to oxidative stress / early endosome membrane / chemical synaptic transmission / perikaryon / negative regulation of neuron apoptotic process / dendritic spine / response to xenobiotic stimulus / membrane raft / apical plasma membrane / 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 | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.34 Å | |||||||||
![]() | Baronina A / Pike ACW | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of human excitatory amino acid transporter 3 (EAAT3) Authors: Baronina A / Pike ACW / Han S / Carpenter EP | |||||||||
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 | ![]() | 28.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 23.3 KB 23.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 7.2 KB | Display | ![]() |
Images | ![]() | 170.1 KB | ||
Masks | ![]() | 30.5 MB | ![]() | |
Filedesc metadata | ![]() | 7.1 KB | ||
Others | ![]() ![]() ![]() | 23 MB 23.4 MB 23.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 881.3 KB | Display | ![]() |
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Full document | ![]() | 880.8 KB | Display | |
Data in XML | ![]() | 12.8 KB | Display | |
Data in CIF | ![]() | 17.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6s3qMC 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
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Annotation | Post-processed RELION map used for building and refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.086 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Additional map: RELION 3D refine map
File | emd_10094_additional.map | ||||||||||||
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Annotation | RELION 3D refine map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: RELION halfmap1
File | emd_10094_half_map_1.map | ||||||||||||
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Annotation | RELION halfmap1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: RELION halfmap2
File | emd_10094_half_map_2.map | ||||||||||||
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Annotation | RELION halfmap2 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : EXCITATORY AMINO ACID TRANSPORTER 3 TRIMER
Entire | Name: EXCITATORY AMINO ACID TRANSPORTER 3 TRIMER |
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Components |
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-Supramolecule #1: EXCITATORY AMINO ACID TRANSPORTER 3 TRIMER
Supramolecule | Name: EXCITATORY AMINO ACID TRANSPORTER 3 TRIMER / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 160 KDa |
-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: ![]() |
Molecular weight | Theoretical: 53.252867 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MGKPARKGCE WKRFLKNNWV LLSTVAAVVL GITTGVLVRE HRNLSTLEKF YFAFPGEILM RMLKLIILPL IISSMITGVA ALDSNVSGK IGVRAVVYYF CTTLIAVILG IVLVVSIKPG VTQKVGEIAR TGSTPEVSTV DAMLDLIRNM FPENLVQACF Q QYKTKREE ...String: MGKPARKGCE WKRFLKNNWV LLSTVAAVVL GITTGVLVRE HRNLSTLEKF YFAFPGEILM RMLKLIILPL IISSMITGVA ALDSNVSGK IGVRAVVYYF CTTLIAVILG IVLVVSIKPG VTQKVGEIAR TGSTPEVSTV DAMLDLIRNM FPENLVQACF Q QYKTKREE VKPPSDPEMN MTEESFTAVM TTAISKNKTK EYKIVGMYSD GINVLGLIVF CLVFGLVIGK MGEKGQILVD FF NALSDAT MKIVQIIMCY MPLGILFLIA GKIIEVEDWE IFRKLGLYMA TVLTGLAIHS IVILPLIYFI VVRKNPFRFA MGM AQALLT ALMISSSSAT LPVTFRCAEE NNQVDKRITR FVLPVGATIN MDGTALYEAV AAVFIAQLND LDLGIGQIIT ISIT ATSAS IGAAGVPQAG LVTMVIVLSA VGLPAEDVTL IIAVDWLLDR FRTMVNVLGD AFGTGIVEKL SKKELEQMDV SSEVN AENL YFQ UniProtKB: Excitatory amino acid transporter 3 |
-Macromolecule #2: (2~{S},3~{S})-2-azanyl-3-[[3-[[4-(trifluoromethyl)phenyl]carbonyl...
Macromolecule | Name: (2~{S},3~{S})-2-azanyl-3-[[3-[[4-(trifluoromethyl)phenyl]carbonylamino]phenyl]methoxy]butanedioic acid type: ligand / ID: 2 / Number of copies: 3 / Formula: 7O9 |
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Molecular weight | Theoretical: 426.343 Da |
Chemical component information | ![]() ChemComp-7O9: |
-Macromolecule #3: CHOLESTEROL HEMISUCCINATE
Macromolecule | Name: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 3 / Number of copies: 3 / Formula: Y01 |
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Molecular weight | Theoretical: 486.726 Da |
Chemical component information | ![]() ChemComp-Y01: |
-Macromolecule #4: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
Macromolecule | Name: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 4 / Number of copies: 15 / Formula: PC1 |
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Molecular weight | Theoretical: 790.145 Da |
Chemical component information | ![]() ChemComp-PC1: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 2 mg/mL | |||||||||||||||||||||
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Buffer | pH: 7.5 Component:
Details: Protein incubated with 1mM TFB-TBOA solution prior to making grids | |||||||||||||||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR | |||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 4.5s. |
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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: SUPER-RESOLUTION / Digitization - Frames/image: 1-48 / Number grids imaged: 1 / Number real images: 3232 / Average exposure time: 12.0 sec. / Average electron dose: 40.7 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Details | Model refined using NCS constraints and rotamer, cbeta restraints only against RELION post-processed b-factor sharpened (-111A**2), 3.34A filtered map |
Refinement | Space: REAL / Protocol: AB INITIO MODEL / Overall B value: 111 / Target criteria: Cross-correlation coefficient |
Output model | ![]() PDB-6s3q: |