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- EMDB-61846: Overall structure of human EAAT2 bound with activator (GT949) -

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Basic information

Entry
Database: EMDB / ID: EMD-61846
TitleOverall structure of human EAAT2 bound with activator (GT949)
Map data
Sample
  • Complex: Overall structure of human EAAT2 in the substrate-free state
    • Protein or peptide: Excitatory amino acid transporter 2
  • Ligand: CHOLESTEROL
  • Ligand: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
  • Ligand: 3-[(~{R})-(4-cyclohexylpiperazin-1-yl)-[1-(2-phenylethyl)-1,2,3,4-tetrazol-5-yl]methyl]-6-methoxy-1~{H}-quinolin-2-one
Keywordstransporter / TRANSPORT PROTEIN
Function / homology
Function and homology information


neurotransmitter reuptake / Astrocytic Glutamate-Glutamine Uptake And Metabolism / membrane protein complex / cysteine transmembrane transporter activity / visual behavior / high-affinity L-glutamate transmembrane transporter activity / glutamate:sodium symporter activity / Transport of inorganic cations/anions and amino acids/oligopeptides / L-glutamate transmembrane transporter activity / L-glutamate transmembrane transport ...neurotransmitter reuptake / Astrocytic Glutamate-Glutamine Uptake And Metabolism / membrane protein complex / cysteine transmembrane transporter activity / visual behavior / high-affinity L-glutamate transmembrane transporter activity / glutamate:sodium symporter activity / Transport of inorganic cations/anions and amino acids/oligopeptides / L-glutamate transmembrane transporter activity / L-glutamate transmembrane transport / glutathione biosynthetic process / D-aspartate import across plasma membrane / L-aspartate transmembrane transport / telencephalon development / monoatomic anion transmembrane transporter activity / L-aspartate import across plasma membrane / Glutamate Neurotransmitter Release Cycle / neutral L-amino acid transmembrane transporter activity / L-glutamate import across plasma membrane / astrocyte projection / transepithelial transport / neuron projection terminus / cellular response to cocaine / neurotransmitter transport / protein homotrimerization / adult behavior / axolemma / response to amino acid / transport across blood-brain barrier / monoatomic ion transport / positive regulation of D-glucose import / multicellular organism growth / response to wounding / presynaptic membrane / cell body / chemical synaptic transmission / vesicle / membrane raft / response to xenobiotic stimulus / glutamatergic synapse / cell surface / metal ion binding / membrane / plasma membrane
Similarity search - Function
: / Sodium:dicarboxylate symporter family signature 2. / Sodium:dicarboxylate symporter / Sodium:dicarboxylate symporter, conserved site / Sodium:dicarboxylate symporter superfamily / Sodium:dicarboxylate symporter family / Sodium:dicarboxylate symporter family signature 1.
Similarity search - Domain/homology
Excitatory amino acid transporter 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.97 Å
AuthorsXia LY / Zhang YY / Shi Y / Huang J / Zhou Q
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971123 China
CitationJournal: Dian Zi Xian Wei Xue Bao / Year: 2025
Title: Structural study of human glutamate transporter EAAT2
Authors: Xia LY / Zhang YY / Shi Y / Huang J / Zhou Q
History
DepositionOct 9, 2024-
Header (metadata) releaseApr 9, 2025-
Map releaseApr 9, 2025-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61846.png

Downloads & links

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Map

FileDownload / File: emd_61846.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 256 pix.
= 275.712 Å		1.08 Å/pix.
x 256 pix.
= 275.712 Å		1.08 Å/pix.
x 256 pix.
= 275.712 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.077 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-1.5249205 - 2.4943733
Average (Standard dev.)0.004757551 (±0.07347275)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 275.712 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61846_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61846_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Overall structure of human EAAT2 in the substrate-free state

EntireName: Overall structure of human EAAT2 in the substrate-free state
Components
  • Complex: Overall structure of human EAAT2 in the substrate-free state
    • Protein or peptide: Excitatory amino acid transporter 2
  • Ligand: CHOLESTEROL
  • Ligand: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
  • Ligand: 3-[(~{R})-(4-cyclohexylpiperazin-1-yl)-[1-(2-phenylethyl)-1,2,3,4-tetrazol-5-yl]methyl]-6-methoxy-1~{H}-quinolin-2-one

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Supramolecule #1: Overall structure of human EAAT2 in the substrate-free state

SupramoleculeName: Overall structure of human EAAT2 in the substrate-free state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Excitatory amino acid transporter 2

MacromoleculeName: Excitatory amino acid transporter 2 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 62.164977 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MASTEGANNM PKQVEVRMHD SHLGSEEPKH RHLGLRLCDK LGKNLLLTLT VFGVILGAVC GGLLRLASPI HPDVVMLIAF PGDILMRML KMLILPLIIS SLITGLSGLD AKASGRLGTR AMVYYMSTTI IAAVLGVILV LAIHPGNPKL KKQLGPGKKN D EVSSLDAF ...String:
MASTEGANNM PKQVEVRMHD SHLGSEEPKH RHLGLRLCDK LGKNLLLTLT VFGVILGAVC GGLLRLASPI HPDVVMLIAF PGDILMRML KMLILPLIIS SLITGLSGLD AKASGRLGTR AMVYYMSTTI IAAVLGVILV LAIHPGNPKL KKQLGPGKKN D EVSSLDAF LDLIRNLFPE NLVQACFQQI QTVTKKVLVA PPPDEEANAT SAVVSLLNET VTEVPEETKM VIKKGLEFKD GM NVLGLIG FFIAFGIAMG KMGDQAKLMV DFFNILNEIV MKLVIMIMWY SPLGIACLIC GKIIAIKDLE VVARQLGMYM VTV IIGLII HGGIFLPLIY FVVTRKNPFS FFAGIFQAWI TALGTASSAG TLPVTFRCLE ENLGIDKRVT RFVLPVGATI NMDG TALYE AVAAIFIAQM NGVVLDGGQI VTVSLTATLA SVGAASIPSA GLVTMLLILT AVGLPTEDIS LLVAVDWLLD RMRTS VNVV GDSFGAGIVY HLSKSELDTI DSQHRVHEDI EMTKTQSIYD DMKNHRESNS NQCVYAAHNS VIVDECKVTL AANGKS ADC SVEEEPWKRE K

UniProtKB: Excitatory amino acid transporter 2

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Macromolecule #2: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 2 / Number of copies: 3 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #3: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE

MacromoleculeName: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / type: ligand / ID: 3 / Number of copies: 3 / Formula: 3PH
Molecular weightTheoretical: 704.998 Da
Chemical component information

ChemComp-3PH:
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE

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Macromolecule #4: 3-[(~{R})-(4-cyclohexylpiperazin-1-yl)-[1-(2-phenylethyl)-1,2,3,4...

MacromoleculeName: 3-[(~{R})-(4-cyclohexylpiperazin-1-yl)-[1-(2-phenylethyl)-1,2,3,4-tetrazol-5-yl]methyl]-6-methoxy-1~{H}-quinolin-2-one
type: ligand / ID: 4 / Number of copies: 3 / Formula: A1EDJ
Molecular weightTheoretical: 527.66 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.97 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.6) / Number images used: 74765
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

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