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- PDB-6x14: Inward-facing state of the glutamate transporter homologue GltPh ... -

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Database: PDB / ID: 6x14
TitleInward-facing state of the glutamate transporter homologue GltPh in complex with TFB-TBOA
ComponentsGlutamate transporter homologue GltPh
KeywordsTRANSPORT PROTEIN / sodium-coupled L-aspartate transporter
Biological speciesPyrococcus horikoshii (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.71 Å
AuthorsWang, X. / Boudker, O.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R37NS085318 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS064357 United States
CitationJournal: Elife / Year: 2020
Title: Large domain movements through the lipid bilayer mediate substrate release and inhibition of glutamate transporters.
Authors: Xiaoyu Wang / Olga Boudker /
Abstract: Glutamate transporters are essential players in glutamatergic neurotransmission in the brain, where they maintain extracellular glutamate below cytotoxic levels and allow for rounds of transmission. ...Glutamate transporters are essential players in glutamatergic neurotransmission in the brain, where they maintain extracellular glutamate below cytotoxic levels and allow for rounds of transmission. The structural bases of their function are well established, particularly within a model archaeal homologue, sodium and aspartate symporter Glt. However, the mechanism of gating on the cytoplasmic side of the membrane remains ambiguous. We report Cryo-EM structures of Glt reconstituted into nanodiscs, including those structurally constrained in the cytoplasm-facing state and either apo, bound to sodium ions only, substrate, or blockers. The structures show that both substrate translocation and release involve movements of the bulky transport domain through the lipid bilayer. They further reveal a novel mode of inhibitor binding and show how solutes release is coupled to protein conformational changes. Finally, we describe how domain movements are associated with the displacement of bound lipids and significant membrane deformations, highlighting the potential regulatory role of the bilayer.
Validation Report
SummaryFull reportAbout validation report
DepositionMay 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release

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Deposited unit
A: Glutamate transporter homologue GltPh
B: Glutamate transporter homologue GltPh
C: Glutamate transporter homologue GltPh
hetero molecules

Theoretical massNumber of molelcules
Total (without water)139,51912

TypeNameSymmetry operationNumber
identity operation1_5551
Buried area7050 Å2
ΔGint-70 kcal/mol
Surface area50270 Å2


#1: Protein Glutamate transporter homologue GltPh

Mass: 44643.918 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-7O9 / (2~{S},3~{S})-2-azanyl-3-[[3-[[4-(trifluoromethyl)phenyl]carbonylamino]phenyl]methoxy]butanedioic acid

Mass: 426.343 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C19H17F3N2O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-6OU / [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate

Mass: 717.996 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C39H76NO8P / Comment: phospholipid*YM
Has ligand of interestY

Experimental details


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

Sample preparation

ComponentName: Complex of inward-facing state of GltPh with TFB-TBOA in MSP1E3 nanodisc
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.134 MDa / Experimental value: NO
Source (natural)Organism: Pyrococcus horikoshii (archaea)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
EM embeddingMaterial: ice
VitrificationCryogen name: ETHANE

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 68.7 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)


SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 3.71 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 75555 / Symmetry type: POINT

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