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- PDB-9jvw: Overall structure of human EAAT2 bound with inhibitor (WAY-213613) -

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Basic information

Entry
Database: PDB / ID: 9jvw
TitleOverall structure of human EAAT2 bound with inhibitor (WAY-213613)
ComponentsExcitatory amino acid transporter 2
KeywordsTRANSPORT PROTEIN / transporter
Function / homology
Function and homology information


neurotransmitter reuptake / Astrocytic Glutamate-Glutamine Uptake And Metabolism / cysteine transmembrane transporter activity / high-affinity L-glutamate transmembrane transporter activity / glutamate:sodium symporter activity / membrane protein complex / visual behavior / : / L-glutamate transmembrane transporter activity / L-glutamate transmembrane transport ...neurotransmitter reuptake / Astrocytic Glutamate-Glutamine Uptake And Metabolism / cysteine transmembrane transporter activity / high-affinity L-glutamate transmembrane transporter activity / glutamate:sodium symporter activity / membrane protein complex / visual behavior / : / L-glutamate transmembrane transporter activity / L-glutamate transmembrane transport / glutathione biosynthetic process / D-aspartate import across plasma membrane / L-aspartate transmembrane transport / monoatomic anion transmembrane transporter activity / telencephalon development / L-aspartate import across plasma membrane / Glutamate Neurotransmitter Release Cycle / neutral L-amino acid transmembrane transporter activity / L-glutamate import across plasma membrane / transepithelial transport / neuron projection terminus / cellular response to cocaine / astrocyte projection / 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 across plasma membrane / response to wounding / multicellular organism growth / presynaptic membrane / cell body / vesicle / chemical synaptic transmission / 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
CHOLESTEROL / Chem-GJ0 / Excitatory amino acid transporter 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.41 Å
AuthorsXia, L.Y. / Zhang, Y.Y. / Shi, Y. / Huang, J. / Zhou, Q.
Funding support China, 1items
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, L.Y. / Zhang, Y.Y. / Shi, Y. / Huang, J. / Zhou, Q.
History
DepositionOct 9, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Excitatory amino acid transporter 2
B: Excitatory amino acid transporter 2
C: Excitatory amino acid transporter 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,9009
Polymers186,4953
Non-polymers2,4066
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Excitatory amino acid transporter 2 / Glutamate/aspartate transporter II / Sodium-dependent glutamate/aspartate transporter 2 / Solute ...Glutamate/aspartate transporter II / Sodium-dependent glutamate/aspartate transporter 2 / Solute carrier family 1 member 2


Mass: 62164.977 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC1A2, EAAT2, GLT1 / Production host: Homo sapiens (human) / References: UniProt: P43004
#2: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H46O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GJ0 / (2S)-2-azanyl-4-[[4-[2-bromanyl-4,5-bis(fluoranyl)phenoxy]phenyl]amino]-4-oxidanylidene-butanoic acid / WAY-213613


Mass: 415.186 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H13BrF2N2O4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Overall structure of human EAAT2 bound with inhibitor (WAY-213613)
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: RELION / Version: 3.0.6 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 207108 / Symmetry type: POINT

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