7XR4 | pdb_00007xr4

Structure of human excitatory amino acid transporter 2 (EAAT2) in complex with glutamate


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7XR4

This is version 1.2 of the entry. See complete history

Literature

Structural basis of ligand binding modes of human EAAT2.

Zhang, Z.Chen, H.Geng, Z.Yu, Z.Li, H.Dong, Y.Zhang, H.Huang, Z.Jiang, J.Zhao, Y.

(2022) Nat Commun 13: 3329-3329

  • DOI: https://doi.org/10.1038/s41467-022-31031-x
  • Primary Citation Related Structures: 
    7XR4, 7XR6

  • PubMed Abstract: 

    In the central nervous system (CNS), excitatory amino acid transporters (EAATs) mediate the uptake of excitatory neurotransmitter glutamate and maintain its low concentrations in the synaptic cleft for avoiding neuronal cytotoxicity. Dysfunction of EAATs can lead to many psychiatric diseases. Here we report cryo-EM structures of human EAAT2 in an inward-facing conformation, in the presence of substrate glutamate or selective inhibitor WAY-213613. The glutamate is coordinated by extensive hydrogen bonds and further stabilized by HP2. The inhibitor WAY-213613 occupies a similar binding pocket to that of the substrate glutamate. Upon association with the WAY-213613, the HP2 undergoes a substantial conformational change, and in turn stabilizes the inhibitor binding by forming hydrophobic interactions. Electrophysiological experiments elucidate that the unique S441 plays pivotal roles in the binding of hEAAT2 with glutamate or WAY-213613, and the I464-L467-V468 cluster acts as a key structural determinant for the selective inhibition of this transporter by WAY-213613.


  • Organizational Affiliation
    • Department of Microbiology and Biotechnology, College of Life Sciences, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, China.

Macromolecule Content 

  • Total Structure Weight: 207.36 kDa 
  • Atom Count: 10,026 
  • Modeled Residue Count: 1,275 
  • Deposited Residue Count: 1,722 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Excitatory amino acid transporter 2
A, B, C
574Homo 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
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PC1

Query on PC1



Download:Ideal Coordinates CCD File
AA [auth C]
BA [auth C]
CA [auth C]
DA [auth C]
EA [auth C]
AA [auth C],
BA [auth C],
CA [auth C],
DA [auth C],
EA [auth C],
F [auth A],
FA [auth C],
G [auth A],
GA [auth C],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
Z [auth C]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
Y01

Query on Y01



Download:Ideal Coordinates CCD File
E [auth A],
O [auth B],
Y [auth C]
CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
GLU
(Subject of Investigation/LOI)

Query on GLU



Download:Ideal Coordinates CCD File
D [auth A],
N [auth B],
X [auth C]
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-22
    Type: Initial release
  • Version 1.1: 2024-07-03
    Changes: Data collection
  • Version 1.2: 2025-07-02
    Changes: Data collection, Structure summary