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- EMDB-52653: Glutamate transporter homologue GltPh mutant P206R in Complex wit... -

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Basic information

Entry
Database: EMDB / ID: EMD-52653
TitleGlutamate transporter homologue GltPh mutant P206R in Complex with L-Aspartate and Sodium Ions in Salipro
Map data
Sample
  • Complex: Glutamate transporter homolog GltPh
    • Protein or peptide: Glutamate transporter homolog
  • Ligand: ASPARTIC ACID
  • Ligand: SODIUM ION
  • Ligand: 1,2-DIOCTANOYL-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL)
  • Ligand: 1-MYRISTOYL-2-HYDROXY-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL)]
  • Ligand: CHLORIDE ION
  • Ligand: (19S,22R,25R)-22,25,26-trihydroxy-16,22-dioxo-17,21,23-trioxa-22lambda~5~-phosphahexacosan-19-yl (9E)-octadec-9-enoate
  • Ligand: water
KeywordsTRANSPORT PROTEIN / Glutamate transport / Salipro / L-aspartate / MEMBRANE PROTEIN
Function / homology
Function and homology information


L-aspartate transmembrane transport / L-aspartate transmembrane transporter activity / amino acid:sodium symporter activity / L-aspartate import across plasma membrane / chloride transmembrane transporter activity / protein homotrimerization / chloride transmembrane transport / metal ion binding / identical protein 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: 3.34 Å
AuthorsHorn G / Overa C / Fu L / Urbansky K / Madej MG / Ziegler C
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)2518 Germany
CitationJournal: To Be Published
Title: CryoEM Structure of Glutamate transporter homologue GltPh mutant P206R in complex with L-Aspartate and Sodium ions in Salipro
Authors: Horn G / Overa C / Fu L / Urbansky K / Madej MG / Ziegler C
History
DepositionJan 29, 2025-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52653.png

Downloads & links

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Map

FileDownload / File: emd_52653.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.79 Å/pix.
x 360 pix.
= 284.076 Å		0.79 Å/pix.
x 360 pix.
= 284.076 Å		0.79 Å/pix.
x 360 pix.
= 284.076 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.7891 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0537
Minimum - Maximum-0.45953456 - 0.713305
Average (Standard dev.)0.0005827558 (±0.0119478945)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 284.076 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52653_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_52653_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_52653_half_map_2.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 : Glutamate transporter homolog GltPh

EntireName: Glutamate transporter homolog GltPh
Components
  • Complex: Glutamate transporter homolog GltPh
    • Protein or peptide: Glutamate transporter homolog
  • Ligand: ASPARTIC ACID
  • Ligand: SODIUM ION
  • Ligand: 1,2-DIOCTANOYL-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL)
  • Ligand: 1-MYRISTOYL-2-HYDROXY-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL)]
  • Ligand: CHLORIDE ION
  • Ligand: (19S,22R,25R)-22,25,26-trihydroxy-16,22-dioxo-17,21,23-trioxa-22lambda~5~-phosphahexacosan-19-yl (9E)-octadec-9-enoate
  • Ligand: water

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Supramolecule #1: Glutamate transporter homolog GltPh

SupramoleculeName: Glutamate transporter homolog GltPh / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Pyrococcus horikoshii (archaea)
Molecular weightTheoretical: 135 KDa

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Macromolecule #1: Glutamate transporter homolog

MacromoleculeName: Glutamate transporter homolog / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus horikoshii (archaea)
Molecular weightTheoretical: 44.870371 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGLYRKYIEY PVLQKILIGL ILGAIVGLIL GHYGYADAVK TYVKPFGDLF VRLLKMLVMP IVFASLVVGA ASISPARLGR VGVKIVVYY LLTSAFAVTL GIIMARLFNP GAGIHLAVGG QQFQPKQAPP LVKILLDIVP TNPFGALANG QVLPTIFFAI I LGIAITYL ...String:
MGLYRKYIEY PVLQKILIGL ILGAIVGLIL GHYGYADAVK TYVKPFGDLF VRLLKMLVMP IVFASLVVGA ASISPARLGR VGVKIVVYY LLTSAFAVTL GIIMARLFNP GAGIHLAVGG QQFQPKQAPP LVKILLDIVP TNPFGALANG QVLPTIFFAI I LGIAITYL MNSENEKVRK SAETLLDAIN GLAEAMYKIV NGVMQYARIG VFALIAYVMA EQGVKVVGEL AKVTAAVYVG LT LQILLVY FVLLKIYGID PISFIKKAKD AMLTAFVTRS SSGTLPVTMR VAKEMGISEG IYSFTLPLGA TINMDGTALY QGV CTFFIA NALGSHLTVG QQLTIVLTAV LASIGTAGVP GAGAIMLAMV LESVGLPLTD PNVAAAYAMI LGIDAILDMG RTMV NVTGD LTGTAIVAKT EGTLEKGVIA

UniProtKB: Glutamate transporter homolog

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Macromolecule #2: ASPARTIC ACID

MacromoleculeName: ASPARTIC ACID / type: ligand / ID: 2 / Number of copies: 3 / Formula: ASP
Molecular weightTheoretical: 133.103 Da
Chemical component information

ChemComp-ASP:
ASPARTIC ACID

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Macromolecule #3: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 3 / Number of copies: 3
Molecular weightTheoretical: 22.99 Da

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Macromolecule #4: 1,2-DIOCTANOYL-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL)

MacromoleculeName: 1,2-DIOCTANOYL-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL) / type: ligand / ID: 4 / Number of copies: 3 / Formula: PG8
Molecular weightTheoretical: 497.537 Da
Chemical component information

ChemComp-PG8:
1,2-DIOCTANOYL-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL)

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Macromolecule #5: 1-MYRISTOYL-2-HYDROXY-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL)]

MacromoleculeName: 1-MYRISTOYL-2-HYDROXY-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL)]
type: ligand / ID: 5 / Number of copies: 3 / Formula: PGM
Molecular weightTheoretical: 483.553 Da
Chemical component information

ChemComp-PGM:
1-MYRISTOYL-2-HYDROXY-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL)]

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Macromolecule #6: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 6 / Number of copies: 6 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #7: (19S,22R,25R)-22,25,26-trihydroxy-16,22-dioxo-17,21,23-trioxa-22l...

MacromoleculeName: (19S,22R,25R)-22,25,26-trihydroxy-16,22-dioxo-17,21,23-trioxa-22lambda~5~-phosphahexacosan-19-yl (9E)-octadec-9-enoate
type: ligand / ID: 7 / Number of copies: 3 / Formula: D3D
Molecular weightTheoretical: 749.007 Da
Chemical component information

ChemComp-D3D:
(19S,22R,25R)-22,25,26-trihydroxy-16,22-dioxo-17,21,23-trioxa-22lambda~5~-phosphahexacosan-19-yl (9E)-octadec-9-enoate

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Macromolecule #8: water

MacromoleculeName: water / type: ligand / ID: 8 / Number of copies: 12 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 7.5
Component:
ConcentrationNameFormula
20.0 mMTrisHCl
150.0 mMNaClNaCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 100 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeJEOL CRYO ARM 200
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 3467 / Average exposure time: 4.1 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 743837
CTF correctionSoftware - Name: CTFFIND (ver. 4.4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6x15

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 249069
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6x15


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: FLEXIBLE FIT
Output model

PDB-9i6d:
Glutamate transporter homologue GltPh mutant P206R in Complex with L-Aspartate and Sodium Ions in Salipro

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