5DWY | pdb_00005dwy

Crystal structure of a substrate-free glutamate transporter homologue GltTk

PDB DOI: https://doi.org/10.2210/pdb5DWY/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Thermococcus kodakarensis KOD1
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD mpstruc

Deposited: 2015-09-23 Released: 2016-09-28
Deposition Author(s): Guskov, A., Slotboom, D.J.
Funding Organization(s): NWO

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.237 (Depositor), 0.241 (DCC)
R-Value Work:
0.198 (Depositor), 0.204 (DCC)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

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 PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/ncomms13420
Primary Citation 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: 144.73 kDa
Atom Count: 10,016
Modeled Residue Count: 1,281
Deposited Residue Count: 1,314
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proton/glutamate symporter, SDF family	A, B, C	438	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JID0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BOG Query on BOG Download:Ideal Coordinates CCD File SDF format, chain R [auth A] SDF format, chain BA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain BA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain BA [auth B]	BA [auth B], R [auth A]	octyl beta-D-glucopyranoside C₁₄ H₂₈ O₆ HEGSGKPQLMEBJL-RKQHYHRCSA-N		Interactions Focus chain BA [auth B] Focus chain R [auth A] Interactions & Density Focus chain BA [auth B] Focus chain R [auth A]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain DA [auth C] SDF format, chain E [auth A] SDF format, chain EA [auth C] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain CA [auth C] MOL2 format, chain D [auth A] MOL2 format, chain DA [auth C] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain CA [auth C] mmCIF format, chain D [auth A] mmCIF format, chain DA [auth C] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain CA [auth C]	CA [auth C] D [auth A] DA [auth C] E [auth A] EA [auth C] CA [auth C], D [auth A], DA [auth C], E [auth A], EA [auth C], F [auth A], G [auth A], H [auth A], I [auth A], S [auth B], T [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain D [auth A] Focus chain DA [auth C] Focus chain E [auth A] Focus chain EA [auth C] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain CA [auth C] Focus chain D [auth A] Focus chain DA [auth C] Focus chain E [auth A] Focus chain EA [auth C] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain S [auth B] Focus chain T [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain IA [auth C] SDF format, chain JA [auth C] SDF format, chain K [auth A] SDF format, chain LA [auth C] SDF format, chain N [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain V [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain U [auth B] SDF format, chain O [auth A] SDF format, chain MA [auth C] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain KA [auth C] SDF format, chain J [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain V [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain U [auth B] MOL2 format, chain O [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain J [auth A] mmCIF format, chain AA [auth B] mmCIF format, chain FA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain JA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain V [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain U [auth B] mmCIF format, chain O [auth A] mmCIF format, chain MA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain J [auth A]	AA [auth B] FA [auth C] GA [auth C] HA [auth C] IA [auth C] AA [auth B], FA [auth C], GA [auth C], HA [auth C], IA [auth C], J [auth A], JA [auth C], K [auth A], KA [auth C], L [auth A], LA [auth C], M [auth A], MA [auth C], N [auth A], O [auth A], P [auth A], Q [auth A], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.237 (Depositor), 0.241 (DCC)
R-Value Work: 0.198 (Depositor), 0.204 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.01	α = 90
b = 116.01	β = 90
c = 308.5	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

View more in-depth experimental data

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: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.4: 2024-01-10
Changes: Data collection, Database references, Refinement description, Structure summary