4KY0 | pdb_00004ky0

Crystal structure of a substrate-free glutamate transporter homologue from Thermococcus kodakarensis

• PDB DOI: https://doi.org/10.2210/pdb4KY0/pdb

• Classification: TRANSPORT PROTEIN, membrane protein
• Organism(s): Thermococcus kodakarensis KOD1
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2013-05-28 Released: 2013-09-11 
• Deposition Author(s): Guskov, A., Jensen, S., Rempel, S., Hanelt, I., Slotboom, D.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.266 (Depositor), 0.275 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a substrate-free aspartate transporter.

Jensen, S., Guskov, A., Rempel, S., Hanelt, I., Slotboom, D.J.

(2013) Nat Struct Mol Biol 20: 1224-1226

• PubMed: 24013209 
• DOI: https://doi.org/10.1038/nsmb.2663
• Primary Citation Related Structures: 
  4KY0


• PubMed Abstract: 
  

  Archaeal glutamate transporter homologs catalyze the coupled uptake of aspartate and three sodium ions. After the delivery of the substrate and sodium ions to the cytoplasm, the empty binding site must reorient to the outward-facing conformation to reset the transporter. Here, we report a crystal structure of the substrate-free transporter GltTk from Thermococcus kodakarensis, which provides insight into the mechanism of this essential step in the translocation cycle.

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Organizational Affiliation: 
• 1] Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands. [2].

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 137.93 kDa 
• Atom Count: 9,360 
• Modeled Residue Count: 1,251 
• Deposited Residue Count: 1,293 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proton/glutamate symporter, SDF family	A, B, C	431	Thermococcus kodakarensis KOD1	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	D [auth A], E [auth B], F [auth C], G [auth C]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.266 (Depositor), 0.275 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.57	α = 90
b = 117.57	β = 90
c = 309.51	γ = 120

Software Package:

Software Name	Purpose
MxCuBE	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-11 
Deposition Author(s): Guskov, A., Jensen, S., Rempel, S., Hanelt, I., Slotboom, D.J.

Revision History  

• Version 1.0: 2013-09-11
  Type: Initial release
  
• Version 1.1: 2013-10-23
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description