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- PDB-31ic: Structure of human excitatory amino acid transporter 3 (EAAT3) in... -

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Basic information

Entry
Database: PDB / ID: 31ic
TitleStructure of human excitatory amino acid transporter 3 (EAAT3) in complex with B11 nanobody
Components
  • B11 nanobody
  • Excitatory amino acid transporter 3
KeywordsMEMBRANE PROTEIN / Transporter / EAAT3 / SLC1A1 / nanobody
Function / homology
Function and homology information


D-aspartate transmembrane transport / regulation of protein targeting to membrane / D-aspartate transmembrane transporter activity / Defective SLC1A1 is implicated in schizophrenia 18 (SCZD18) and dicarboxylic aminoaciduria (DCBXA) / distal dendrite / L-cysteine transport / L-cysteine transmembrane transporter activity / L-glutamate import / high-affinity L-glutamate transmembrane transporter activity / glutamate:sodium symporter activity ...D-aspartate transmembrane transport / regulation of protein targeting to membrane / D-aspartate transmembrane transporter activity / Defective SLC1A1 is implicated in schizophrenia 18 (SCZD18) and dicarboxylic aminoaciduria (DCBXA) / distal dendrite / L-cysteine transport / L-cysteine transmembrane transporter activity / L-glutamate import / high-affinity L-glutamate transmembrane transporter activity / glutamate:sodium symporter activity / neurotransmitter receptor transport to plasma membrane / response to decreased oxygen levels / : / cellular response to mercury ion / retina layer formation / L-glutamate transmembrane transporter activity / glutathione biosynthetic process / L-glutamate transmembrane transport / L-aspartate transmembrane transport / righting reflex / cellular response to ammonium ion / zinc ion transmembrane transport / L-aspartate transmembrane transporter activity / intracellular glutamate homeostasis / Glutamate Neurotransmitter Release Cycle / L-aspartate import across plasma membrane / grooming behavior / cellular response to bisphenol A / D-aspartate import across plasma membrane / proximal dendrite / monoatomic anion channel activity / L-glutamate import across plasma membrane / intracellular zinc ion homeostasis / transepithelial transport / apical dendrite / chloride transmembrane transporter activity / blood vessel morphogenesis / cellular response to cocaine / motor neuron apoptotic process / G protein-coupled dopamine receptor signaling pathway / response to anesthetic / superoxide metabolic process / glutamate receptor signaling pathway / response to morphine / perisynaptic space / heart contraction / neurotransmitter transport / maintenance of blood-brain barrier / dopamine metabolic process / motor behavior / adult behavior / asymmetric synapse / glial cell projection / response to axon injury / conditioned place preference / postsynaptic modulation of chemical synaptic transmission / positive regulation of heart rate / transport across blood-brain barrier / behavioral fear response / synaptic cleft / monoatomic ion transport / neurogenesis / axon terminus / chloride transmembrane transport / cell periphery / dendritic shaft / response to amphetamine / locomotory behavior / brain development / synapse organization / recycling endosome / Schaffer collateral - CA1 synapse / recycling endosome membrane / memory / cytokine-mediated signaling pathway / apical part of cell / long-term synaptic potentiation / late endosome membrane / presynapse / cellular response to oxidative stress / early endosome membrane / gene expression / dendritic spine / chemical synaptic transmission / negative regulation of neuron apoptotic process / perikaryon / apical plasma membrane / membrane raft / response to xenobiotic stimulus / axon / neuronal cell body / synapse / dendrite / cell surface / extracellular exosome / membrane / metal ion binding / identical protein 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
Excitatory amino acid transporter 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Vicugna pacos (alpaca)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsLi, A. / Pike, A.C.W. / Baronina, A. / Rodstrom, K.E.J. / Pascoa, T.C. / Chi, G. / Stefanic, S. / Carpenter, E.P. / Bullock, A.N. / Dong, Y.Y. / Sauer, D.B.
Funding support United Kingdom, Switzerland, 3items
OrganizationGrant numberCountry
Wellcome Trust102161/Z/13/Z United Kingdom
Innovative Medicines Initiative777372 Switzerland
Innovative Medicines Initiative875510 Switzerland
CitationJournal: To Be Published
Title: Structure of human excitatory amino acid transporter 3 (EAAT3) in complex with a nanobody
Authors: Li, A. / Pike, A.C.W. / Baronina, A. / Rodstrom, K.E.J. / Pascoa, T.C. / Chi, G. / Stefanic, S. / Carpenter, E.P. / Bullock, A.N. / Dong, Y.Y. / Sauer, D.B.
History
DepositionJun 5, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Mask / Part number: 2 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 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

Downloads & links

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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
D: B11 nanobody


Theoretical massNumber of molelcules
Total (without water)177,9774
Polymers177,9774
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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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: 53182.750 Da / Num. of mol.: 3 / Mutation: L92V
Source method: isolated from a genetically manipulated source
Details: Missing residues at 488-506 are due to proteolytic cleavage by TEV protease. Other missing regions are unresolved.
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC1A1, EAAC1, EAAT3, HEAAC1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P43005
#2: Antibody B11 nanobody


Mass: 18429.158 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Missing regions are unresolved / Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli MC1061 (bacteria)
Has protein modificationY

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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: human excitatory amino acid transporter 3 (EAAT3) in complex with B11 nanobody
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
Details: 20 mM HEPES pH 7.5, 150 mM NaCl, 0.003% LMNG, 0.0003% CHS
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
2150 mMsodium chlorideNaCl1
30.003 %Lauryl Maltose Neopentyl GlycolC47H88O221
40.0003 %Cholesteryl hemisuccinateC31H50O41
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: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Details: Objective aperture 100 um; data collected on eBIC-Diamond Krios III microscope
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 8.32 sec. / Electron dose: 38.55 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3056
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
1cryoSPARC3.3.1particle selection
4cryoSPARC3.3.1CTF correction
7Coot0.9.8.93model fitting
9cryoSPARC3.3.1initial Euler assignment
10cryoSPARC3.3.1final Euler assignment
11cryoSPARC3.3.1classification
12cryoSPARC3.3.13D reconstruction
13PHENIX1.21.1_5286model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 132709 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: real space refinement
Details: initial model fitted with 6S3Q for EAAT3 and 1ZVH for B11 nanobody in COOT. Model was refined in Phenix.
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-IDAccession codeChain-IDInitial refinement model-ID
16S3Q

6s3q

A6S3QA1
21ZVH

1zvh

B1ZVHB2
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 50.34 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002310180
ELECTRON MICROSCOPYf_angle_d0.467813903
ELECTRON MICROSCOPYf_chiral_restr0.03841807
ELECTRON MICROSCOPYf_plane_restr0.00371697
ELECTRON MICROSCOPYf_dihedral_angle_d11.7523408

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