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- EMDB-21987: Inward-facing sodium-bound state of the glutamate transporter hom... -

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Basic information

Entry
Database: EMDB / ID: EMD-21987
TitleInward-facing sodium-bound state of the glutamate transporter homologue GltPh
Map data
Sample
  • Complex: Complex of inward-facing sodium-bound state of GltPh in MSP1E3 nanodisc
    • Protein or peptide: Glutamate transporter homologue GltPh
  • Ligand: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate
Keywordssodium-coupled L-aspartate transporter / TRANSPORT PROTEIN
Function / homology
Function and homology information


amino acid:sodium symporter activity / L-aspartate transmembrane transport / L-aspartate transmembrane transporter activity / L-aspartate import across plasma membrane / chloride transmembrane transporter activity / protein homotrimerization / chloride transmembrane transport / identical protein binding / metal ion binding / plasma membrane
Similarity search - Function
Sodium:dicarboxylate symporter / Sodium:dicarboxylate symporter, conserved site / Sodium:dicarboxylate symporter superfamily / Sodium:dicarboxylate symporter family / Sodium:dicarboxylate symporter family signature 1.
Similarity search - Domain/homology
Glutamate transporter homolog
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.66 Å
AuthorsWang X / Boudker O
Funding support United States, 2 items
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 homolog, 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.
History
DepositionMay 18, 2020-
Header (metadata) releaseNov 18, 2020-
Map releaseNov 18, 2020-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6x13
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21987.png

Downloads & links

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Map

FileDownload / File: emd_21987.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.)
1.07 Å/pix.
x 256 pix.
= 274.752 Å		1.07 Å/pix.
x 256 pix.
= 274.752 Å		1.07 Å/pix.
x 256 pix.
= 274.752 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07325 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0345 / Movie #1: 0.05
Minimum - Maximum-0.15859205 - 0.26101786
Average (Standard dev.)0.00010409822 (±0.0034193203)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 274.752 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.073251.073251.07325
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z274.752274.752274.752
α/β/γ90.00090.00090.000
start NX/NY/NZ714763
NX/NY/NZ169194164
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.1590.2610.000

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Supplemental data

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Sample components

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Entire : Complex of inward-facing sodium-bound state of GltPh in MSP1E3 na...

EntireName: Complex of inward-facing sodium-bound state of GltPh in MSP1E3 nanodisc
Components
  • Complex: Complex of inward-facing sodium-bound state of GltPh in MSP1E3 nanodisc
    • Protein or peptide: Glutamate transporter homologue GltPh
  • Ligand: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate

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Supramolecule #1: Complex of inward-facing sodium-bound state of GltPh in MSP1E3 na...

SupramoleculeName: Complex of inward-facing sodium-bound state of GltPh in MSP1E3 nanodisc
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Pyrococcus horikoshii (archaea)
Molecular weightTheoretical: 134 KDa

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Macromolecule #1: Glutamate transporter homologue GltPh

MacromoleculeName: Glutamate transporter homologue GltPh / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus horikoshii (archaea)
Molecular weightTheoretical: 44.643918 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: (FME)GLYRKYIEY PVLQKILIGL ILGAIVGLIL GHYGYAHAVH TYVKPFGDLF VRLLCMLVMP IVFASLVVGA ASISPA RLG RVGVKIVVYY LLTSAFAVTL GIIMARLFNP GAGIHLAVGG QQFQPHQAPP LVHILLDIVP TNPFGALANG QVLPTIF FA IILGIAITYL ...String:
(FME)GLYRKYIEY PVLQKILIGL ILGAIVGLIL GHYGYAHAVH TYVKPFGDLF VRLLCMLVMP IVFASLVVGA ASISPA RLG RVGVKIVVYY LLTSAFAVTL GIIMARLFNP GAGIHLAVGG QQFQPHQAPP LVHILLDIVP TNPFGALANG QVLPTIF FA IILGIAITYL MNSENEKVRK SAETLLDAIN GLAEAMYKIV NGVMQYAPIG VFALIAYVMA EQGVHVVGEL AKVTAAVY V GLTLQILLVY FVLLKIYGID PISFIKHAKD AMLTAFVTRS SSGTLPVTMR VAKEMGISEG IYSFTLPLGA TINMDGTAL YQGVATFFIA NALGSHLTVG QQLTIVLTAV LASIGTAGVP GAGAIMLCMV LHSVGLPLTD PNVAAAYAMI LGIDAILDMG RTMVNVTGD LTGTAIVAKT EGTLVPR

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Macromolecule #2: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyl...

MacromoleculeName: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate
type: ligand / ID: 2 / Number of copies: 1 / Formula: 6OU
Molecular weightTheoretical: 717.996 Da
Chemical component information

ChemComp-6OU:
[(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate / phospholipid*YM

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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
Sugar embeddingMaterial: ice
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 68.55 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.66 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 191349
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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