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- EMDB-52657: EAAT1 thermostabilized mutant in Complex with L-Asp, Metal Ions, ... -

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Basic information

Entry
Database: EMDB / ID: EMD-52657
TitleEAAT1 thermostabilized mutant in Complex with L-Asp, Metal Ions, and the allosteric inhibitor UCPH101 in Salipro
Map data
Sample
  • Complex: Excitatory amino acid transporter 1, SLC1A3
    • Protein or peptide: EAAT1 thermostabilized mutant
  • Ligand: 2-Amino-5,6,7,8-tetrahydro-4-(4-methoxyphenyl)-7-(naphthalen-1-yl)-5-oxo-4H-chromene-3-carbonitrile
  • Ligand: ASPARTIC ACID
  • Ligand: SODIUM ION
  • Ligand: water
KeywordsTRANSPORT PROTEIN / Glutamate transport / Salipro / L-aspartate / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.12 Å
AuthorsHorn G / Fu L / 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 EAAT1 thermostabilized mutant in Complex with L-Asp, Metal Ions, and the allosteric inhibitor UCPH101 in Salipro
Authors: Horn G / Fu L / Madej MG / Ziegler C
History
DepositionJan 31, 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_52657.png

Downloads & links

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Map

FileDownload / File: emd_52657.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.)
0.79 Å/pix.
x 256 pix.
= 202.01 Å		0.79 Å/pix.
x 256 pix.
= 202.01 Å		0.79 Å/pix.
x 256 pix.
= 202.01 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: 0.203
Minimum - Maximum-1.6041958 - 2.0065722
Average (Standard dev.)0.0014412808 (±0.049057882)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 202.0096 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52657_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_52657_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_52657_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 : Excitatory amino acid transporter 1, SLC1A3

EntireName: Excitatory amino acid transporter 1, SLC1A3
Components
  • Complex: Excitatory amino acid transporter 1, SLC1A3
    • Protein or peptide: EAAT1 thermostabilized mutant
  • Ligand: 2-Amino-5,6,7,8-tetrahydro-4-(4-methoxyphenyl)-7-(naphthalen-1-yl)-5-oxo-4H-chromene-3-carbonitrile
  • Ligand: ASPARTIC ACID
  • Ligand: SODIUM ION
  • Ligand: water

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Supramolecule #1: Excitatory amino acid transporter 1, SLC1A3

SupramoleculeName: Excitatory amino acid transporter 1, SLC1A3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: EAAT1 thermostabilized mutant
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 169 KDa

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Macromolecule #1: EAAT1 thermostabilized mutant

MacromoleculeName: EAAT1 thermostabilized mutant / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 56.512379 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MTKSNGEEPK MGGRMERFQQ GVSKRTLLAK KKVQNITKED VKSFLRRNAL LLLTVLAVIL GVVLGFLLRP YPLSPREVKY FAFPGELLM RMLKMLILPL IVSSLITGLA SLDAKASGRL GMRAVVYYMS TTIIAVVLGI ILVLIIHPGA ASAAITASVG A AGSAENAP ...String:
MTKSNGEEPK MGGRMERFQQ GVSKRTLLAK KKVQNITKED VKSFLRRNAL LLLTVLAVIL GVVLGFLLRP YPLSPREVKY FAFPGELLM RMLKMLILPL IVSSLITGLA SLDAKASGRL GMRAVVYYMS TTIIAVVLGI ILVLIIHPGA ASAAITASVG A AGSAENAP SKEVLDCFLD LARNIFPSNL VSAAFRSYST TYEERTITGT RVKVPVGQEV EGMNILGLVV FSMVFGFALG KM GEQGQLL VDFFNSLNEA TMKLVAIIMW YAPLGILFLI AGKIVEMEDL EVLGGQLGMY MVTVIVGLVI HGLIVLPLIY FLI TRKNPF VFIAGILQAL ITALGTSSSS ATLPITFKCL EENNGVDKRI TRFVLPVGAT INMDGTALYE AVAAIFIAQV NNYE LDFGQ IITISITATA ASIGAAGIPQ AGLVTMVIVL TAVGLPTDDI TLIIAVDWLL DRFRTMVNVL GDALGAGIVE HLSRK ELEK QDAELGNSVI EENEMKKPYQ LIAQDNETEK PIDSETKM

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Macromolecule #2: 2-Amino-5,6,7,8-tetrahydro-4-(4-methoxyphenyl)-7-(naphthalen-1-yl...

MacromoleculeName: 2-Amino-5,6,7,8-tetrahydro-4-(4-methoxyphenyl)-7-(naphthalen-1-yl)-5-oxo-4H-chromene-3-carbonitrile
type: ligand / ID: 2 / Number of copies: 3 / Formula: 6Z6
Molecular weightTheoretical: 422.475 Da
Chemical component information

ChemComp-6Z6:
2-Amino-5,6,7,8-tetrahydro-4-(4-methoxyphenyl)-7-(naphthalen-1-yl)-5-oxo-4H-chromene-3-carbonitrile

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Macromolecule #3: ASPARTIC ACID

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

ChemComp-ASP:
ASPARTIC ACID

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Macromolecule #4: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 4 / Number of copies: 9
Molecular weightTheoretical: 22.99 Da

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 6 / 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: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL CRYO ARM 200
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 11159 / Average exposure time: 6.89 sec. / Average electron dose: 61.29 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 / 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: 3980401
CTF correctionSoftware - Name: CTFFIND (ver. 4.4.11) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5llm

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. V4) / Number images used: 435981
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. V4)
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. V4)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5llm


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9i7m:
EAAT1 thermostabilized mutant in Complex with L-Asp, Metal Ions, and the allosteric inhibitor UCPH101 in Salipro

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