7AWQ | pdb_00007awq

Structure of the thermostabilized EAAT1 cryst-E386Q mutant in complex with L-ASP, sodium ions and the allosteric inhibitor UCPH101


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.65 Å
  • R-Value Free: 
    0.271 (Depositor), 0.339 (DCC) 
  • R-Value Work: 
    0.233 (Depositor), 0.263 (DCC) 
  • R-Value Observed: 
    0.235 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

The ion-coupling mechanism of human excitatory amino acid transporters.

Canul-Tec, J.C.Kumar, A.Dhenin, J.Assal, R.Legrand, P.Rey, M.Chamot-Rooke, J.Reyes, N.

(2022) EMBO J 41: e108341-e108341

  • DOI: https://doi.org/10.15252/embj.2021108341
  • Primary Citation Related Structures: 
    7AWL, 7AWM, 7AWN, 7AWP, 7AWQ, 7NPW

  • PubMed Abstract: 

    Excitatory amino acid transporters (EAATs) maintain glutamate gradients in the brain essential for neurotransmission and to prevent neuronal death. They use ionic gradients as energy source and co-transport transmitter into the cytoplasm with Na + and H + , while counter-transporting K + to re-initiate the transport cycle. However, the molecular mechanisms underlying ion-coupled transport remain incompletely understood. Here, we present 3D X-ray crystallographic and cryo-EM structures, as well as thermodynamic analysis of human EAAT1 in different ion bound conformations, including elusive counter-transport ion bound states. Binding energies of Na + and H + , and unexpectedly Ca 2+ , are coupled to neurotransmitter binding. Ca 2+ competes for a conserved Na + site, suggesting a regulatory role for Ca 2+ in glutamate transport at the synapse, while H + binds to a conserved glutamate residue stabilizing substrate occlusion. The counter-transported ion binding site overlaps with that of glutamate, revealing the K + -based mechanism to exclude the transmitter during the transport cycle and to prevent its neurotoxic release on the extracellular side.


  • Organizational Affiliation
    • Membrane Protein Mechanisms Unit, Institut Pasteur, Paris, France.

Macromolecule Content 

  • Total Structure Weight: 57.25 kDa 
  • Atom Count: 3,118 
  • Modeled Residue Count: 404 
  • Deposited Residue Count: 522 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Excitatory amino acid transporter 1,Neutral amino acid transporter B(0),Excitatory amino acid transporter 1522Homo sapiensMutation(s): 0 
Gene Names: SLC1A3EAAT1GLASTGLAST1SLC1A5ASCT2M7V1RDRRDRC
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P43003 (Homo sapiens)
Explore P43003 
Go to UniProtKB:  P43003
PHAROS:  P43003
GTEx:  ENSG00000079215 
Find proteins for Q15758 (Homo sapiens)
Explore Q15758 
Go to UniProtKB:  Q15758
PHAROS:  Q15758
GTEx:  ENSG00000105281 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP43003Q15758
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6Z6
(Subject of Investigation/LOI)

Query on 6Z6



Download:Ideal Coordinates CCD File
E [auth A]2-Amino-5,6,7,8-tetrahydro-4-(4-methoxyphenyl)-7-(naphthalen-1-yl)-5-oxo-4H-chromene-3-carbonitrile
C27 H22 N2 O3
YBMGNDPBARCLFT-YDONVPIESA-N
BA

Query on BA



Download:Ideal Coordinates CCD File
F [auth A]BARIUM ION
Ba
XDFCIPNJCBUZJN-UHFFFAOYSA-N
ASP

Query on ASP



Download:Ideal Coordinates CCD File
D [auth A]ASPARTIC ACID
C4 H7 N O4
CKLJMWTZIZZHCS-REOHCLBHSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.65 Å
  • R-Value Free:  0.271 (Depositor), 0.339 (DCC) 
  • R-Value Work:  0.233 (Depositor), 0.263 (DCC) 
  • R-Value Observed: 0.235 (Depositor) 
Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124α = 90
b = 124β = 90
c = 90.81γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)France309657

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-13
    Type: Initial release
  • Version 1.1: 2021-12-01
    Changes: Database references
  • Version 1.2: 2022-01-12
    Changes: Database references
  • Version 1.3: 2022-01-19
    Changes: Database references
  • Version 1.4: 2024-01-31
    Changes: Data collection, Refinement description