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- PDB-9i6d: Glutamate transporter homologue GltPh mutant P206R in Complex wit... -

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Basic information

Entry
Database: PDB / ID: 9i6d
TitleGlutamate transporter homologue GltPh mutant P206R in Complex with L-Aspartate and Sodium Ions in Salipro
ComponentsGlutamate transporter homolog
KeywordsMEMBRANE PROTEIN / TRANSPORT PROTEIN / Glutamate transport / Salipro / L-aspartate
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
ASPARTIC ACID / Chem-D3D / Chem-PG8 / Chem-PGM / Glutamate transporter homolog
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.34 Å
AuthorsHorn, G. / Overa, C. / Fu, L. / Urbansky, K. / 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 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, M.G. / Ziegler, C.
History
DepositionJan 29, 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: Glutamate transporter homolog
B: Glutamate transporter homolog
C: Glutamate transporter homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,48224
Polymers134,6113
Non-polymers5,87121
Water21612
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)336.06548, 90.04852
3given(-0.5, 0.866025), (-0.866025, -0.5), (1)90.04851, 336.06547

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Glutamate transporter homolog / Glt(Ph) / Sodium-aspartate symporter Glt(Ph) / Sodium-dependent aspartate transporter


Mass: 44870.371 Da / Num. of mol.: 3 / Mutation: P206R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: PH1295 / Production host: Escherichia coli (E. coli) / References: UniProt: O59010

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Non-polymers , 7 types, 33 molecules

#2: Chemical ChemComp-ASP / ASPARTIC ACID


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


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PG8 / 1,2-DIOCTANOYL-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL)


Mass: 497.537 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C22H42O10P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PGM / 1-MYRISTOYL-2-HYDROXY-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL)] / LYSOPHOSPHATIDYLGLYCEROL


Mass: 483.553 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C22H44O9P / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#7: Chemical 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


Mass: 749.007 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C40H77O10P / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

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Details

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: Glutamate transporter homolog GltPh / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.135 MDa / Experimental value: NO
Source (natural)Organism: Pyrococcus horikoshii (archaea)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTrisHCl1
2150 mMNaClNaCl1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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 / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: JEOL CRYOSPECPORTER
Image recordingAverage exposure time: 4.1 sec. / Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3467
Image scansMovie frames/image: 37

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Processing

EM software
IDNameVersionCategory
2SerialEMimage acquisition
4CTFFIND4.4CTF correction
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
11cryoSPARCclassification
12cryoSPARC3D reconstruction
13REFMAC5model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 743837
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 249069 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT
Atomic model buildingPDB-ID: 6x15

6x15


Accession code: 6x15 / Source name: PDB / Type: experimental model
RefinementResolution: 3.34→123.1 Å / Cor.coef. Fo:Fc: 0.575 / SU B: 37.1 / SU ML: 0.569 / ESU R: 0.413
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.49411 --
obs0.49411 62431 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 47.185 Å2
Refinement stepCycle: 1 / Total: 3129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0060.0123167
ELECTRON MICROSCOPYr_bond_other_d00.0163301
ELECTRON MICROSCOPYr_angle_refined_deg1.3841.7924290
ELECTRON MICROSCOPYr_angle_other_deg0.4351.6887580
ELECTRON MICROSCOPYr_dihedral_angle_1_deg4.1295407
ELECTRON MICROSCOPYr_dihedral_angle_2_deg27.57515
ELECTRON MICROSCOPYr_dihedral_angle_3_deg15.94610519
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.0530.2540
ELECTRON MICROSCOPYr_gen_planes_refined0.0040.023470
ELECTRON MICROSCOPYr_gen_planes_other0.0010.02630
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_it2.9154.4221634
ELECTRON MICROSCOPYr_mcbond_other2.9144.4231634
ELECTRON MICROSCOPYr_mcangle_it5.0837.9382039
ELECTRON MICROSCOPYr_mcangle_other5.0827.9372040
ELECTRON MICROSCOPYr_scbond_it3.8865.2591533
ELECTRON MICROSCOPYr_scbond_other3.8855.2621534
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other6.9179.3992252
ELECTRON MICROSCOPYr_long_range_B_refined13.19252.0412792
ELECTRON MICROSCOPYr_long_range_B_other13.19252.0412793
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3.34→3.427 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork1.245 4659 -
obs--100 %

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