6R7R | pdb_00006r7r

Crystal structure of the glutamate transporter homologue GltTk in complex with D-aspartate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.269 (Depositor), 0.279 (DCC) 
  • R-Value Work: 
    0.232 (Depositor), 0.241 (DCC) 
  • R-Value Observed: 
    0.234 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6R7R

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Binding and transport of D-aspartate by the glutamate transporter homolog Glt Tk .

Arkhipova, V.Trinco, G.Ettema, T.W.Jensen, S.Slotboom, D.J.Guskov, A.

(2019) Elife 8

  • DOI: https://doi.org/10.7554/eLife.45286
  • Primary Citation Related Structures: 
    6R7R

  • PubMed Abstract: 

    Mammalian glutamate transporters are crucial players in neuronal communication as they perform neurotransmitter reuptake from the synaptic cleft. Besides L-glutamate and L-aspartate, they also recognize D-aspartate, which might participate in mammalian neurotransmission and/or neuromodulation. Much of the mechanistic insight in glutamate transport comes from studies of the archeal homologs Glt Ph from Pyrococcus horikoshii and Glt Tk from Thermococcus kodakarensis . Here, we show that Glt Tk transports D-aspartate with identical Na + : substrate coupling stoichiometry as L-aspartate, and that the affinities ( K d and K m ) for the two substrates are similar. We determined a crystal structure of Glt Tk with bound D-aspartate at 2.8 Å resolution. Comparison of the L- and D-aspartate bound Glt Tk structures revealed that D-aspartate is accommodated with only minor rearrangements in the structure of the binding site. The structure explains how the geometrically different molecules L- and D-aspartate are recognized and transported by the protein in the same way.


  • Organizational Affiliation
    • Groningen Biomolecular Sciences and Biotechnology Institute, Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands.

Macromolecule Content 

  • Total Structure Weight: 143.87 kDa 
  • Atom Count: 9,512 
  • Modeled Residue Count: 1,244 
  • Deposited Residue Count: 1,314 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Proton/glutamate symporter, SDF family
A, B, C
438Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: TK0986
Membrane Entity: Yes 
UniProt
Find proteins for Q5JID0 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Explore Q5JID0 
Go to UniProtKB:  Q5JID0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5JID0
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DMU

Query on DMU



Download:Ideal Coordinates CCD File
L [auth A]DECYL-BETA-D-MALTOPYRANOSIDE
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N
P6G

Query on P6G



Download:Ideal Coordinates CCD File
V [auth B],
W [auth B]
HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
1PE

Query on 1PE



Download:Ideal Coordinates CCD File
Z [auth B]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
PG4

Query on PG4



Download:Ideal Coordinates CCD File
K [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE

Query on PGE



Download:Ideal Coordinates CCD File
M [auth A],
X [auth B],
Y [auth B]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
DAS
(Subject of Investigation/LOI)

Query on DAS



Download:Ideal Coordinates CCD File
DA [auth C],
G [auth A],
Q [auth B]
D-ASPARTIC ACID
C4 H7 N O4
CKLJMWTZIZZHCS-UWTATZPHSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
EA [auth C]
FA [auth C]
GA [auth C]
H [auth A]
HA [auth C]
EA [auth C],
FA [auth C],
GA [auth C],
H [auth A],
HA [auth C],
I [auth A],
IA [auth C],
J [auth A],
R [auth B],
S [auth B],
T [auth B],
U [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
AA [auth C]
BA [auth C]
CA [auth C]
D [auth A]
E [auth A]
AA [auth C],
BA [auth C],
CA [auth C],
D [auth A],
E [auth A],
F [auth A],
N [auth B],
O [auth B],
P [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.269 (Depositor), 0.279 (DCC) 
  • R-Value Work:  0.232 (Depositor), 0.241 (DCC) 
  • R-Value Observed: 0.234 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.55α = 90
b = 116.55β = 90
c = 314.77γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Netherlands Organisation for Scientific ResearchNetherlands865.11.001

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-17
    Type: Initial release
  • Version 1.1: 2019-05-01
    Changes: Data collection, Database references
  • Version 1.2: 2020-09-30
    Changes: Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Refinement description