5E9S

Crystal structure of substrate-bound glutamate transporter homologue GltTk

PDB DOI: https://doi.org/10.2210/pdb5E9S/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Thermococcus kodakarensis
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes OPMPDBTMmpstruc

Deposited: 2015-10-15 Released: 2016-09-28
Deposition Author(s): Guskov, A., Slotboom, D.J.
Funding Organization(s): NWO

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.242
R-Value Work: 0.213
R-Value Observed: 0.214

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 8AFA

Literature

Coupled binding mechanism of three sodium ions and aspartate in the glutamate transporter homologue GltTk.

Guskov, A., Jensen, S., Faustino, I., Marrink, S.J., Slotboom, D.J.

(2016) Nat Commun 7: 13420-13420

PubMed: 27830699 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/ncomms13420
Primary Citation of Related Structures:
5DWY, 5E9S

PubMed Abstract:
Glutamate transporters catalyse the thermodynamically unfavourable transport of anionic amino acids across the cell membrane by coupling it to the downhill transport of cations. This coupling mechanism is still poorly understood, in part because the available crystal structures of these transporters are of relatively low resolution. Here we solve crystal structures of the archaeal transporter Glt _Tk in the presence and absence of aspartate and use molecular dynamics simulations and binding assays to show how strict coupling between the binding of three sodium ions and aspartate takes place.

Organizational Affiliation

University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, Nijenborgh 4, 9747 AG Groningen, The Netherlands.

Macromolecule Content

Total Structure Weight: 149.74 kDa
Atom Count: 10,213
Modelled Residue Count: 1,280
Deposited Residue Count: 1,314
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proton/glutamate symporter, SDF family	A, B, C	438	Thermococcus kodakarensis	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5JID0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DMU Query on DMU Download Ideal Coordinates CCD File SDF format, chain CB [auth C] SDF format, chain DA [auth B] SDF format, chain H [auth A] MOL2 format, chain CB [auth C] MOL2 format, chain DA [auth B] MOL2 format, chain H [auth A] mmCIF format, chain CB [auth C] mmCIF format, chain DA [auth B] mmCIF format, chain H [auth A]	CB [auth C], DA [auth B], H [auth A]	DECYL-BETA-D-MALTOPYRANOSIDE C₂₂ H₄₂ O₁₁ WOQQAWHSKSSAGF-WXFJLFHKSA-N		Interactions Focus chain CB [auth C] Focus chain DA [auth B] Focus chain H [auth A] Interactions & Density Focus chain CB [auth C] Focus chain DA [auth B] Focus chain H [auth A]
P6G Query on P6G Download Ideal Coordinates CCD File SDF format, chain QB [auth C] SDF format, chain RB [auth C] SDF format, chain WA [auth B] SDF format, chain XA [auth B] SDF format, chain Y [auth A] MOL2 format, chain QB [auth C] MOL2 format, chain RB [auth C] MOL2 format, chain WA [auth B] MOL2 format, chain XA [auth B] MOL2 format, chain Y [auth A] mmCIF format, chain QB [auth C] mmCIF format, chain RB [auth C] mmCIF format, chain WA [auth B] mmCIF format, chain XA [auth B] mmCIF format, chain Y [auth A]	QB [auth C], RB [auth C], WA [auth B], XA [auth B], Y [auth A]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain QB [auth C] Focus chain RB [auth C] Focus chain WA [auth B] Focus chain XA [auth B] Focus chain Y [auth A] Interactions & Density Focus chain QB [auth C] Focus chain RB [auth C] Focus chain WA [auth B] Focus chain XA [auth B] Focus chain Y [auth A]
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain DB [auth C] SDF format, chain EA [auth B] SDF format, chain EB [auth C] SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain DB [auth C] MOL2 format, chain EA [auth B] MOL2 format, chain EB [auth C] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] mmCIF format, chain DB [auth C] mmCIF format, chain EA [auth B] mmCIF format, chain EB [auth C] mmCIF format, chain FA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A]	DB [auth C] EA [auth B] EB [auth C] FA [auth B] GA [auth B] DB [auth C], EA [auth B], EB [auth C], FA [auth B], GA [auth B], I [auth A], J [auth A]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain DB [auth C] Focus chain EA [auth B] Focus chain EB [auth C] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain DB [auth C] Focus chain EA [auth B] Focus chain EB [auth C] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain I [auth A] Focus chain J [auth A]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain OB [auth C] SDF format, chain PB [auth C] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain VA [auth B] SDF format, chain W [auth A] SDF format, chain X [auth A] MOL2 format, chain OB [auth C] MOL2 format, chain PB [auth C] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth B] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] mmCIF format, chain OB [auth C] mmCIF format, chain PB [auth C] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A] mmCIF format, chain VA [auth B] mmCIF format, chain W [auth A] mmCIF format, chain X [auth A]	OB [auth C] PB [auth C] U [auth A] V [auth A] VA [auth B] OB [auth C], PB [auth C], U [auth A], V [auth A], VA [auth B], W [auth A], X [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain OB [auth C] Focus chain PB [auth C] Focus chain U [auth A] Focus chain V [auth A] Focus chain VA [auth B] Focus chain W [auth A] Focus chain X [auth A] Interactions & Density Focus chain OB [auth C] Focus chain PB [auth C] Focus chain U [auth A] Focus chain V [auth A] Focus chain VA [auth B] Focus chain W [auth A] Focus chain X [auth A]
ASP Query on ASP Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain YA [auth C] SDF format, chain Z [auth B] MOL2 format, chain D [auth A] MOL2 format, chain YA [auth C] MOL2 format, chain Z [auth B] mmCIF format, chain D [auth A] mmCIF format, chain YA [auth C] mmCIF format, chain Z [auth B]	D [auth A], YA [auth C], Z [auth B]	ASPARTIC ACID C₄ H₇ N O₄ CKLJMWTZIZZHCS-REOHCLBHSA-N		Interactions Focus chain D [auth A] Focus chain YA [auth C] Focus chain Z [auth B] Interactions & Density Focus chain D [auth A] Focus chain YA [auth C] Focus chain Z [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain FB [auth C] SDF format, chain GB [auth C] SDF format, chain HA [auth B] SDF format, chain HB [auth C] SDF format, chain IA [auth B] SDF format, chain IB [auth C] SDF format, chain JA [auth B] SDF format, chain JB [auth C] SDF format, chain K [auth A] SDF format, chain KA [auth B] SDF format, chain KB [auth C] SDF format, chain L [auth A] SDF format, chain LA [auth B] SDF format, chain LB [auth C] SDF format, chain M [auth A] SDF format, chain MA [auth B] SDF format, chain MB [auth C] SDF format, chain N [auth A] SDF format, chain NA [auth B] SDF format, chain NB [auth C] SDF format, chain O [auth A] SDF format, chain OA [auth B] SDF format, chain P [auth A] SDF format, chain PA [auth B] SDF format, chain Q [auth A] SDF format, chain QA [auth B] SDF format, chain R [auth A] SDF format, chain RA [auth B] SDF format, chain S [auth A] SDF format, chain SA [auth B] SDF format, chain T [auth A] SDF format, chain TA [auth B] SDF format, chain UA [auth B] MOL2 format, chain FB [auth C] MOL2 format, chain GB [auth C] MOL2 format, chain HA [auth B] MOL2 format, chain HB [auth C] MOL2 format, chain IA [auth B] MOL2 format, chain IB [auth C] MOL2 format, chain JA [auth B] MOL2 format, chain JB [auth C] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain KB [auth C] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain LB [auth C] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain MB [auth C] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain NB [auth C] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain UA [auth B] mmCIF format, chain FB [auth C] mmCIF format, chain GB [auth C] mmCIF format, chain HA [auth B] mmCIF format, chain HB [auth C] mmCIF format, chain IA [auth B] mmCIF format, chain IB [auth C] mmCIF format, chain JA [auth B] mmCIF format, chain JB [auth C] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain KB [auth C] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth B] mmCIF format, chain LB [auth C] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain MB [auth C] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth B] mmCIF format, chain NB [auth C] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth B] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth B] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth B] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth B] mmCIF format, chain UA [auth B]	FB [auth C] GB [auth C] HA [auth B] HB [auth C] IA [auth B] FB [auth C], GB [auth C], HA [auth B], HB [auth C], IA [auth B], IB [auth C], JA [auth B], JB [auth C], K [auth A], KA [auth B], KB [auth C], L [auth A], LA [auth B], LB [auth C], M [auth A], MA [auth B], MB [auth C], N [auth A], NA [auth B], NB [auth C], O [auth A], OA [auth B], P [auth A], PA [auth B], Q [auth A], QA [auth B], R [auth A], RA [auth B], S [auth A], SA [auth B], T [auth A], TA [auth B], UA [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain FB [auth C] Focus chain GB [auth C] Focus chain HA [auth B] Focus chain HB [auth C] Focus chain IA [auth B] Focus chain IB [auth C] Focus chain JA [auth B] Focus chain JB [auth C] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth C] Focus chain L [auth A] Focus chain LA [auth B] Focus chain LB [auth C] Focus chain M [auth A] Focus chain MA [auth B] Focus chain MB [auth C] Focus chain N [auth A] Focus chain NA [auth B] Focus chain NB [auth C] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain UA [auth B] Interactions & Density Focus chain FB [auth C] Focus chain GB [auth C] Focus chain HA [auth B] Focus chain HB [auth C] Focus chain IA [auth B] Focus chain IB [auth C] Focus chain JA [auth B] Focus chain JB [auth C] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth C] Focus chain L [auth A] Focus chain LA [auth B] Focus chain LB [auth C] Focus chain M [auth A] Focus chain MA [auth B] Focus chain MB [auth C] Focus chain N [auth A] Focus chain NA [auth B] Focus chain NB [auth C] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain UA [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain AB [auth C] SDF format, chain BA [auth B] SDF format, chain BB [auth C] SDF format, chain CA [auth B] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain ZA [auth C] MOL2 format, chain AA [auth B] MOL2 format, chain AB [auth C] MOL2 format, chain BA [auth B] MOL2 format, chain BB [auth C] MOL2 format, chain CA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain ZA [auth C] mmCIF format, chain AA [auth B] mmCIF format, chain AB [auth C] mmCIF format, chain BA [auth B] mmCIF format, chain BB [auth C] mmCIF format, chain CA [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain ZA [auth C]	AA [auth B] AB [auth C] BA [auth B] BB [auth C] CA [auth B] AA [auth B], AB [auth C], BA [auth B], BB [auth C], CA [auth B], E [auth A], F [auth A], G [auth A], ZA [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain AB [auth C] Focus chain BA [auth B] Focus chain BB [auth C] Focus chain CA [auth B] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain ZA [auth C] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth C] Focus chain BA [auth B] Focus chain BB [auth C] Focus chain CA [auth B] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain ZA [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.242
R-Value Work: 0.213
R-Value Observed: 0.214
Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.52	α = 90
b = 117.52	β = 90
c = 310.59	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2016-09-28

Deposition Author(s):

Guskov, A.

Slotboom, D.J.

Funding Organization	Location	Grant Number
NWO	Netherlands	865.11.001

Revision History (Full details and data files)

Version 1.0: 2016-09-28
Type: Initial release
Version 1.1: 2016-11-16
Changes: Database references
Version 1.2: 2016-11-23
Changes: Database references
Version 1.3: 2024-01-10
Changes: Data collection, Database references, Refinement description