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- EMDB-21986: Inward-facing Apo-open state of the glutamate transporter homolog... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-21986 | |||||||||
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Title | Inward-facing Apo-open state of the glutamate transporter homologue GltPh | |||||||||
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![]() | sodium-coupled L-aspartate transporter / TRANSPORT PROTEIN | |||||||||
Function / homology | ![]() 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 | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.52 Å | |||||||||
![]() | Wang X / Boudker O | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 3.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 11 KB 11 KB | Display Display | ![]() |
Images | ![]() | 37.9 KB | ||
Filedesc metadata | ![]() | 5.3 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6x12MC ![]() 6x13C ![]() 6x14C ![]() 6x15C ![]() 6x16C ![]() 6x17C C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.07325 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Complex of inward-facing Apo-open state of GltPh in MSP1E3 nanodisc
Entire | Name: Complex of inward-facing Apo-open state of GltPh in MSP1E3 nanodisc |
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Components |
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-Supramolecule #1: Complex of inward-facing Apo-open state of GltPh in MSP1E3 nanodisc
Supramolecule | Name: Complex of inward-facing Apo-open state of GltPh in MSP1E3 nanodisc type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 134 KDa |
-Macromolecule #1: Glutamate transporter homologue GltPh
Macromolecule | Name: Glutamate transporter homologue GltPh / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 44.643918 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: (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 |
-Macromolecule #2: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyl...
Macromolecule | Name: [(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 |
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Molecular weight | Theoretical: 717.996 Da |
Chemical component information | ![]() ChemComp-6OU: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Sugar embedding | Material: ice |
Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 68.55 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: PDB ENTRY |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 148582 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |