Inward-facing structure of human EAAT2 in the WAY213613-bound state

Experimental Data Snapshot

  • Resolution: 3.49 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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Structural insights into inhibitory mechanism of human excitatory amino acid transporter EAAT2.

Kato, T.Kusakizako, T.Jin, C.Zhou, X.Ohgaki, R.Quan, L.Xu, M.Okuda, S.Kobayashi, K.Yamashita, K.Nishizawa, T.Kanai, Y.Nureki, O.

(2022) Nat Commun 13: 4714-4714

  • DOI: https://doi.org/10.1038/s41467-022-32442-6
  • Primary Citation of Related Structures:  
    7VR7, 7VR8

  • PubMed Abstract: 

    Glutamate is a pivotal excitatory neurotransmitter in mammalian brains, but excessive glutamate causes numerous neural disorders. Almost all extracellular glutamate is retrieved by the glial transporter, Excitatory Amino Acid Transporter 2 (EAAT2), belonging to the SLC1A family. However, in some cancers, EAAT2 expression is enhanced and causes resistance to therapies by metabolic disturbance. Despite its crucial roles, the detailed structural information about EAAT2 has not been available. Here, we report cryo-EM structures of human EAAT2 in substrate-free and selective inhibitor WAY213613-bound states at 3.2 Å and 2.8 Å, respectively. EAAT2 forms a trimer, with each protomer consisting of transport and scaffold domains. Along with a glutamate-binding site, the transport domain possesses a cavity that could be disrupted during the transport cycle. WAY213613 occupies both the glutamate-binding site and cavity of EAAT2 to interfere with its alternating access, where the sensitivity is defined by the inner environment of the cavity. We provide the characterization of the molecular features of EAAT2 and its selective inhibition mechanism that may facilitate structure-based drug design for EAAT2.

  • Organizational Affiliation

    Department of Biological Science, Graduate School of Science, The University of Tokyo, Tokyo, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Excitatory amino acid transporter 2581Homo sapiensMutation(s): 0 
Gene Names: SLC1A2EAAT2GLT1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P43004 (Homo sapiens)
Explore P43004 
Go to UniProtKB:  P43004
PHAROS:  P43004
GTEx:  ENSG00000110436 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43004
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PC1

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A]
C44 H88 N O8 P
Query on 9Z9

Download Ideal Coordinates CCD File 
C [auth A](3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en
C34 H56 O5
GJ0 (Subject of Investigation/LOI)
Query on GJ0

Download Ideal Coordinates CCD File 
B [auth A](2S)-2-azanyl-4-[[4-[2-bromanyl-4,5-bis(fluoranyl)phenoxy]phenyl]amino]-4-oxidanylidene-butanoic acid
C16 H13 Br F2 N2 O4
CLR (Subject of Investigation/LOI)
Query on CLR

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
C27 H46 O
Experimental Data & Validation

Experimental Data

  • Resolution: 3.49 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-10
    Type: Initial release
  • Version 1.1: 2022-09-28
    Changes: Database references