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- EMDB-10632: Structure of glutamate transporter homologue GltTk in the presenc... -

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Basic information

Entry
Database: EMDB / ID: EMD-10632
TitleStructure of glutamate transporter homologue GltTk in the presence of TBOA inhibitor
Map data
Sample
  • Complex: Trimer of GltTk
    • Protein or peptide: Proton/glutamate symporter, SDF family
  • Ligand: (3S)-3-(BENZYLOXY)-L-ASPARTIC ACID
KeywordsAMINO ACID TRANSPORTER / ASPARTATE TRANSPORT / GLUTAMATE TRANSPORTER HOMOLOGUE / TRANSPORT PROTEIN / MEMBRANE PROTEIN
Function / homologycarboxylic acid transport / Sodium:dicarboxylate symporter / Sodium:dicarboxylate symporter, conserved site / Sodium:dicarboxylate symporter superfamily / Sodium:dicarboxylate symporter family / Sodium:dicarboxylate symporter family signature 1. / symporter activity / membrane / Proton/glutamate symporter, SDF family
Function and homology information
Biological speciesThermococcus kodakarensis KOD1 (archaea) / Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.47 Å
AuthorsArkhipova V / Slotboom DJ
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, 2020-
Header (metadata) releaseFeb 5, 2020-
Map releaseMar 4, 2020-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.13
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.13
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6xwn
  • Surface level: 0.13
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10632.png

Downloads & links

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Map

FileDownload / File: emd_10632.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 256 pix.
= 259.072 Å		1.01 Å/pix.
x 256 pix.
= 259.072 Å		1.01 Å/pix.
x 256 pix.
= 259.072 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.012 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.102 / Movie #1: 0.13
Minimum - Maximum-0.17094076 - 0.4420258
Average (Standard dev.)0.0021305138 (±0.017637713)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 259.072 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0121.0121.012
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z259.072259.072259.072
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.1710.4420.002

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Supplemental data

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Additional map: sharpened map

Fileemd_10632_additional.map
Annotationsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Trimer of GltTk

EntireName: Trimer of GltTk
Components
  • Complex: Trimer of GltTk
    • Protein or peptide: Proton/glutamate symporter, SDF family
  • Ligand: (3S)-3-(BENZYLOXY)-L-ASPARTIC ACID

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Supramolecule #1: Trimer of GltTk

SupramoleculeName: Trimer of GltTk / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Thermococcus kodakarensis KOD1 (archaea)
Molecular weightTheoretical: 136 KDa

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Macromolecule #1: Proton/glutamate symporter, SDF family

MacromoleculeName: Proton/glutamate symporter, SDF family / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea)
Molecular weightTheoretical: 45.580203 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGKSLLRRYL DYPVLWKILW GLVLGAVFGL IAGHFGYAGA VKTYIKPFGD LFVRLLKMLV MPIVLASLVV GAASISPARL GRVGVKIVV YYLATSAMAV FFGLIVGRLF NVGANVNLGS GTGKAIEAQP PSLVQTLLNI VPTNPFASLA KGEVLPVIFF A IILGIAIT ...String:
MGKSLLRRYL DYPVLWKILW GLVLGAVFGL IAGHFGYAGA VKTYIKPFGD LFVRLLKMLV MPIVLASLVV GAASISPARL GRVGVKIVV YYLATSAMAV FFGLIVGRLF NVGANVNLGS GTGKAIEAQP PSLVQTLLNI VPTNPFASLA KGEVLPVIFF A IILGIAIT YLMNRNEERV RKSAETLLRV FDGLAEAMYL IVGGVMQYAP IGVFALIAYV MAEQGVRVVG PLAKVVGAVY TG LFLQIVI TYFILLKVFG IDPIKFIRKA KDAMITAFVT RSSSGTLPVT MRVAEEEMGV DKGIFSFTLP LGATINMDGT ALY QGVTVL FVANAIGHPL TLGQQLVVVL TAVLASIGTA GVPGAGAIML AMVLQSVGLD LTPGSPVALA YAMILGIDAI LDMG RTMVN VTGDLAGTVI VAKTEKELDE SKWIS

UniProtKB: Proton/glutamate symporter, SDF family

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Macromolecule #2: (3S)-3-(BENZYLOXY)-L-ASPARTIC ACID

MacromoleculeName: (3S)-3-(BENZYLOXY)-L-ASPARTIC ACID / type: ligand / ID: 2 / Number of copies: 2 / Formula: TB1
Molecular weightTheoretical: 239.225 Da
Chemical component information

ChemComp-TB1:
(3S)-3-(BENZYLOXY)-L-ASPARTIC ACID

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 53.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 132917
Initial angle assignmentType: OTHER
Final angle assignmentType: NOT APPLICABLE

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