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- PDB-9i7m: EAAT1 thermostabilized mutant in Complex with L-Asp, Metal Ions, ... -

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Basic information

Entry
Database: PDB / ID: 9i7m
TitleEAAT1 thermostabilized mutant in Complex with L-Asp, Metal Ions, and the allosteric inhibitor UCPH101 in Salipro
ComponentsEAAT1 thermostabilized mutant
KeywordsMEMBRANE PROTEIN / TRANSPORT PROTEIN / Glutamate transport / Salipro / L-aspartate
Function / homologyChem-6Z6 / ASPARTIC ACID
Function and homology information
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.12 Å
AuthorsHorn, G. / Fu, L. / Madej, M.G. / Ziegler, C.
Funding support Germany, 1items
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, M.G. / Ziegler, C.
History
DepositionJan 31, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EAAT1 thermostabilized mutant
C: EAAT1 thermostabilized mutant
E: EAAT1 thermostabilized mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,41118
Polymers169,5373
Non-polymers1,87415
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.5, -0.866025), (0.866025, -0.5), (1)238.9799, 64.03449
3given(-0.5, 0.866025), (-0.866025, -0.5), (1)64.0345, 238.9799

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Components

#1: Protein EAAT1 thermostabilized mutant


Mass: 56512.379 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Chemical ChemComp-6Z6 / 2-Amino-5,6,7,8-tetrahydro-4-(4-methoxyphenyl)-7-(naphthalen-1-yl)-5-oxo-4H-chromene-3-carbonitrile


Mass: 422.475 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H22N2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H7NO4
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Excitatory amino acid transporter 1, SLC1A3 / Type: COMPLEX / Details: EAAT1 thermostabilized mutant / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.169 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 200
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 600 nm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: JEOL CRYOSPECPORTER
Image recordingAverage exposure time: 6.89 sec. / Electron dose: 61.29 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 11159
EM imaging opticsEnergyfilter name: In-column Omega Filter / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1RELION4particle selection
2SerialEMimage acquisition
4CTFFIND4.4.11CTF correction
7UCSF Chimeramodel fitting
9RELION4initial Euler assignment
10cryoSPARCV4final Euler assignment
11cryoSPARCV4classification
12cryoSPARCV43D reconstruction
13REFMAC5model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3980401
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 435981 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 5LLM

5llm


Accession code: 5LLM / Source name: PDB / Type: experimental model
RefinementResolution: 3.12→3.12 Å / Cor.coef. Fo:Fc: 0.582 / SU B: 31.1 / SU ML: 0.509 / ESU R: 0.339
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.46846 --
obs0.46846 69648 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 32.893 Å2
Refinement stepCycle: 1 / Total: 3114
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0060.0123162
ELECTRON MICROSCOPYr_bond_other_d00.0163238
ELECTRON MICROSCOPYr_angle_refined_deg1.471.7854307
ELECTRON MICROSCOPYr_angle_other_deg0.5371.6937389
ELECTRON MICROSCOPYr_dihedral_angle_1_deg5.0155407
ELECTRON MICROSCOPYr_dihedral_angle_2_deg10.087520
ELECTRON MICROSCOPYr_dihedral_angle_3_deg15.06610528
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.0770.2548
ELECTRON MICROSCOPYr_gen_planes_refined0.0050.023565
ELECTRON MICROSCOPYr_gen_planes_other0.0010.02677
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it2.2663.171641
ELECTRON MICROSCOPYr_mcbond_other2.2663.1711641
ELECTRON MICROSCOPYr_mcangle_it4.0265.6822043
ELECTRON MICROSCOPYr_mcangle_other4.0255.6812044
ELECTRON MICROSCOPYr_scbond_it2.8543.6221521
ELECTRON MICROSCOPYr_scbond_other2.8543.6231520
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other5.1416.5342265
ELECTRON MICROSCOPYr_long_range_B_refined10.30936.4613096
ELECTRON MICROSCOPYr_long_range_B_other10.30836.4613097
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3.1→3.181 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork2.279 5145 -
obs--100 %

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