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- PDB-6s3q: Structure of human excitatory amino acid transporter 3 (EAAT3) in... -

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Basic information

Entry
Database: PDB / ID: 6s3q
TitleStructure of human excitatory amino acid transporter 3 (EAAT3) in complex with TFB-TBOA
ComponentsExcitatory amino acid transporter 3
KeywordsMEMBRANE PROTEIN / GLUTAMATE / ASPARTATE TRANSPORTER / CYSTEINE / INHIBITOR COMPLEX / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


D-aspartate transmembrane transport / response to anesthetic / regulation of protein targeting to membrane / D-aspartate transmembrane transporter activity / Defective SLC1A1 is implicated in schizophrenia 18 (SCZD18) and dicarboxylic aminoaciduria (DCBXA) / response to decreased oxygen levels / distal dendrite / cysteine transmembrane transporter activity / cysteine transport / high-affinity L-glutamate transmembrane transporter activity ...D-aspartate transmembrane transport / response to anesthetic / regulation of protein targeting to membrane / D-aspartate transmembrane transporter activity / Defective SLC1A1 is implicated in schizophrenia 18 (SCZD18) and dicarboxylic aminoaciduria (DCBXA) / response to decreased oxygen levels / distal dendrite / cysteine transmembrane transporter activity / cysteine transport / high-affinity L-glutamate transmembrane transporter activity / glutamate:sodium symporter activity / L-glutamate import / neurotransmitter receptor transport to plasma membrane / cellular response to mercury ion / Transport of inorganic cations/anions and amino acids/oligopeptides / zinc ion transmembrane transport / retina layer formation / L-glutamate transmembrane transport / L-glutamate transmembrane transporter activity / monoatomic anion channel activity / cellular response to bisphenol A / L-aspartate transmembrane transport / D-aspartate import across plasma membrane / cellular response to ammonium ion / proximal dendrite / glutathione biosynthetic process / righting reflex / L-aspartate transmembrane transporter activity / L-aspartate import across plasma membrane / grooming behavior / intracellular glutamate homeostasis / Glutamate Neurotransmitter Release Cycle / L-glutamate import across plasma membrane / conditioned place preference / transepithelial transport / apical dendrite / intracellular zinc ion homeostasis / glutamate receptor signaling pathway / response to morphine / neurotransmitter transport / cellular response to cocaine / blood vessel morphogenesis / motor behavior / motor neuron apoptotic process / glutamate binding / chloride transmembrane transporter activity / G protein-coupled dopamine receptor signaling pathway / adult behavior / positive regulation of heart rate / postsynaptic modulation of chemical synaptic transmission / maintenance of blood-brain barrier / dopamine metabolic process / superoxide metabolic process / heart contraction / perisynaptic space / glial cell projection / cellular response to organic cyclic compound / transport across blood-brain barrier / asymmetric synapse / response to axon injury / behavioral fear response / monoatomic ion transport / synaptic cleft / axon terminus / chloride transmembrane transport / response to amphetamine / neurogenesis / dendritic shaft / locomotory behavior / cell periphery / long-term synaptic potentiation / synapse organization / regulation of protein phosphorylation / Schaffer collateral - CA1 synapse / brain development / memory / cytokine-mediated signaling pathway / recycling endosome membrane / presynapse / late endosome membrane / gene expression / early endosome membrane / cellular response to oxidative stress / chemical synaptic transmission / perikaryon / negative regulation of neuron apoptotic process / dendritic spine / response to xenobiotic stimulus / membrane raft / apical plasma membrane / axon / neuronal cell body / dendrite / cell surface / endoplasmic reticulum / extracellular exosome / identical protein binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Sodium:dicarboxylate symporter family signature 2. / 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
Chem-7O9 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / CHOLESTEROL HEMISUCCINATE / Excitatory amino acid transporter 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.34 Å
AuthorsBaronina, A. / Pike, A.C.W. / Yu, X. / Dong, Y.Y. / Shintre, C.A. / Tessitore, A. / Chu, A. / Rotty, B. / Venkaya, S. / Mukhopadhyay, S. ...Baronina, A. / Pike, A.C.W. / Yu, X. / Dong, Y.Y. / Shintre, C.A. / Tessitore, A. / Chu, A. / Rotty, B. / Venkaya, S. / Mukhopadhyay, S. / Borkowska, O. / Chalk, R. / Shrestha, L. / Burgess-Brown, N.A. / Edwards, A.M. / Arrowsmith, C.H. / Bountra, C. / Han, S. / Carpenter, E.P. / Structural Genomics Consortium (SGC)
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust106169/Z/14/Z United Kingdom
Biotechnology and Biological Sciences Research Council United Kingdom
CitationJournal: TO BE PUBLISHED
Title: Structure of human excitatory amino acid transporter 3 (EAAT3)
Authors: Baronina, A. / Pike, A.C.W. / Han, S. / Carpenter, E.P.
History
DepositionJun 25, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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Assembly

Deposited unit
A: Excitatory amino acid transporter 3
B: Excitatory amino acid transporter 3
C: Excitatory amino acid transporter 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,35024
Polymers159,7593
Non-polymers14,59121
Water00
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area19470 Å2
ΔGint-183 kcal/mol
Surface area54520 Å2
MethodPISA

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Components

#1: Protein Excitatory amino acid transporter 3 / Excitatory amino-acid carrier 1 / Neuronal and epithelial glutamate transporter / Sodium-dependent ...Excitatory amino-acid carrier 1 / Neuronal and epithelial glutamate transporter / Sodium-dependent glutamate/aspartate transporter 3 / Solute carrier family 1 member 1


Mass: 53252.867 Da / Num. of mol.: 3 / Mutation: S42R, L92V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC1A1, EAAC1, EAAT3 / Plasmid: pFB-CT10HF-LIC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P43005
#2: Chemical ChemComp-7O9 / (2~{S},3~{S})-2-azanyl-3-[[3-[[4-(trifluoromethyl)phenyl]carbonylamino]phenyl]methoxy]butanedioic acid


Mass: 426.343 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C19H17F3N2O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C31H50O4
#4: Chemical
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
Has ligand of interestY

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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 3 TRIMER / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.16 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm) / Plasmid: pFB-CT10HF-LIC
Buffer solutionpH: 7.5
Details: Protein incubated with 1mM TFB-TBOA solution prior to making grids
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
2150 mMsodium chlorideNaCl1
30.003 % (w/v)Lauryl Maltose Neopentyl GlycolC47H88O221
40.0003 % (w/v)Cholesteryl hemisuccinateC31H50O41
51 mMTFB-TBOAC19H17F3N2O61
60.01 % (w/v)dodecyl-beta-D-maltosideC24H46O111
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 K / Details: blot for 4.5s

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 12 sec. / Electron dose: 40.7 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3232
Image scansMovie frames/image: 48 / Used frames/image: 1-48

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Processing

SoftwareName: PHENIX / Version: 1.14_3260: / Classification: refinement
EM software
IDNameVersionCategory
2SerialEMimage acquisition
4CTFFIND4.1.10CTF correction
7UCSF Chimera1.11model fitting
8Coot0.8.9.1model fitting
10RELION3initial Euler assignment
11RELION3final Euler assignment
12RELION3classification
13RELION33D reconstruction
14PHENIX1.14model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 281809
Details: Particles were picked based on 2D templates arising from classification of particles picked from a subset of images using gautomatch in non-template mode.
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 113258 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 111 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Cross-correlation coefficient
Details: Model refined using NCS constraints and rotamer, cbeta restraints only against RELION post-processed b-factor sharpened (-111A**2), 3.34A filtered map
Atomic model buildingPDB-ID: 6GCT

6gct


Pdb chain-ID: A / Accession code: 6GCT / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01110428
ELECTRON MICROSCOPYf_angle_d0.95714088
ELECTRON MICROSCOPYf_dihedral_angle_d6.8586366
ELECTRON MICROSCOPYf_chiral_restr0.061746
ELECTRON MICROSCOPYf_plane_restr0.0071680

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