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- PDB-6xwn: Structure of glutamate transporter homologue GltTk in the presenc... -

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Entry
Database: PDB / ID: 6xwn
TitleStructure of glutamate transporter homologue GltTk in the presence of TBOA inhibitor
ComponentsProton/glutamate symporter, SDF family
KeywordsTRANSPORT PROTEIN / AMINO ACID TRANSPORTER / ASPARTATE TRANSPORT / GLUTAMATE TRANSPORTER HOMOLOGUE / MEMBRANE PROTEIN
Function / homology
Function and homology information


carboxylic acid transport / symporter activity / membrane / plasma membrane
Similarity search - Function
Proton glutamate symport protein / Sodium:dicarboxylate symporter / Sodium:dicarboxylate symporter / Sodium:dicarboxylate symporter, conserved site / Sodium:dicarboxylate symporter superfamily / Sodium:dicarboxylate symporter family / Sodium:dicarboxylate symporter family signature 1. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
(3S)-3-(BENZYLOXY)-L-ASPARTIC ACID / Proton/glutamate symporter, SDF family
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.47 Å
AuthorsArkhipova, V. / Slotboom, D.J. / Guskov, A.
CitationJournal: Nat Commun / Year: 2020
Title: Structural ensemble of a glutamate transporter homologue in lipid nanodisc environment.
Authors: Valentina Arkhipova / Albert Guskov / Dirk J Slotboom /
Abstract: Glutamate transporters are cation-coupled secondary active membrane transporters that clear the neurotransmitter L-glutamate from the synaptic cleft. These transporters are homotrimers, with each ...Glutamate transporters are cation-coupled secondary active membrane transporters that clear the neurotransmitter L-glutamate from the synaptic cleft. These transporters are homotrimers, with each protomer functioning independently by an elevator-type mechanism, in which a mobile transport domain alternates between inward- and outward-oriented states. Using single-particle cryo-EM we have determined five structures of the glutamate transporter homologue Glt, a Na- L-aspartate symporter, embedded in lipid nanodiscs. Dependent on the substrate concentrations used, the protomers of the trimer adopt a variety of asymmetrical conformations, consistent with the independent movement. Six of the 15 resolved protomers are in a hitherto elusive state of the transport cycle in which the inward-facing transporters are loaded with Na ions. These structures explain how substrate-leakage is prevented - a strict requirement for coupled transport. The belt protein of the lipid nanodiscs bends around the inward oriented protomers, suggesting that membrane deformations occur during transport.
History
DepositionJan 24, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2020Data content type: Additional map / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2020Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2020Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2020Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2020Data content type: Additional map / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2020Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2020Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2020Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jul 9, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details
Item: _em_admin.last_update / _em_software.name / _pdbx_entry_details.has_protein_modification
Revision 1.1Jul 9, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Assembly

Deposited unit
A: Proton/glutamate symporter, SDF family
B: Proton/glutamate symporter, SDF family
C: Proton/glutamate symporter, SDF family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,2195
Polymers136,7413
Non-polymers4782
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area8090 Å2
ΔGint-54 kcal/mol
Surface area47690 Å2
MethodPISA

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Components

#1: Protein Proton/glutamate symporter, SDF family


Mass: 45580.203 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea)
Gene: TK0986 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JID0
#2: Chemical ChemComp-TB1 / (3S)-3-(BENZYLOXY)-L-ASPARTIC ACID / D,L-THREO-BENZYLOXYASPARTATE


Mass: 239.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H13NO5
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Trimer of GltTk / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.136 MDa / Experimental value: YES
Source (natural)Organism: Thermococcus kodakarensis KOD1 (archaea)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 53 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 132917 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0049724
ELECTRON MICROSCOPYf_angle_d0.55813234
ELECTRON MICROSCOPYf_dihedral_angle_d16.8811361
ELECTRON MICROSCOPYf_chiral_restr0.0391647
ELECTRON MICROSCOPYf_plane_restr0.0051626

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