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- EMDB-58427: Structure of human excitatory amino acid transporter 3 (EAAT3) in... -

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Basic information

Entry
Database: EMDB / ID: EMD-58427
TitleStructure of human excitatory amino acid transporter 3 (EAAT3) in complex with B11 nanobody
Map datasharpened to B-factor of -147.8 A
Sample
  • Complex: human excitatory amino acid transporter 3 (EAAT3) in complex with B11 nanobody
    • Protein or peptide: Excitatory amino acid transporter 3
    • Protein or peptide: B11 nanobody
KeywordsTransporter / EAAT3 / SLC1A1 / nanobody / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human) / Vicugna pacos (alpaca)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsLi A / Pike ACW / Baronina A / Rodstrom KEJ / Pascoa TC / Chi G / Stefanic S / Carpenter EP / Bullock AN / Dong YY / Sauer DB
Funding support United Kingdom, Switzerland, 3 items
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 ACW / Baronina A / Rodstrom KEJ / Pascoa TC / Chi G / Stefanic S / Carpenter EP / Bullock AN / Dong YY / Sauer DB
History
DepositionJun 5, 2026-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_58427.png

Downloads & links

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Map

FileDownload / File: emd_58427.map.gz / Format: CCP4 / Size: 75.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened to B-factor of -147.8 A
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 270 pix.
= 248.67 Å		0.92 Å/pix.
x 270 pix.
= 248.67 Å		0.92 Å/pix.
x 270 pix.
= 248.67 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.921 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.29
Minimum - Maximum-1.5209335 - 2.5327146
Average (Standard dev.)0.0034586317 (±0.06350633)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions270270270
Spacing270270270
CellA=B=C: 248.67 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_58427_msk_1.map
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Mask #2

Fileemd_58427_msk_2.map
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Additional map: unsharpened map

Fileemd_58427_additional_1.map
Annotationunsharpened map
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Half map: #2

Fileemd_58427_half_map_1.map
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Half map: #1

Fileemd_58427_half_map_2.map
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Sample components

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Entire : human excitatory amino acid transporter 3 (EAAT3) in complex with...

EntireName: human excitatory amino acid transporter 3 (EAAT3) in complex with B11 nanobody
Components
  • Complex: human excitatory amino acid transporter 3 (EAAT3) in complex with B11 nanobody
    • Protein or peptide: Excitatory amino acid transporter 3
    • Protein or peptide: B11 nanobody

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Supramolecule #1: human excitatory amino acid transporter 3 (EAAT3) in complex with...

SupramoleculeName: human excitatory amino acid transporter 3 (EAAT3) in complex with B11 nanobody
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Excitatory amino acid transporter 3

MacromoleculeName: Excitatory amino acid transporter 3 / type: protein_or_peptide / ID: 1
Details: Missing residues at 488-506 are due to proteolytic cleavage by TEV protease. Other missing regions are unresolved.
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 53.18275 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGKPARKGCE WKRFLKNNWV LLSTVAAVVL GITTGVLVRE HSNLSTLEKF YFAFPGEILM RMLKLIILPL IISSMITGVA ALDSNVSGK IGVRAVVYYF CTTLIAVILG IVLVVSIKPG VTQKVGEIAR TGSTPEVSTV DAMLDLIRNM FPENLVQACF Q QYKTKREE ...String:
MGKPARKGCE WKRFLKNNWV LLSTVAAVVL GITTGVLVRE HSNLSTLEKF YFAFPGEILM RMLKLIILPL IISSMITGVA ALDSNVSGK IGVRAVVYYF CTTLIAVILG IVLVVSIKPG VTQKVGEIAR TGSTPEVSTV DAMLDLIRNM FPENLVQACF Q QYKTKREE VKPPSDPEMN MTEESFTAVM TTAISKNKTK EYKIVGMYSD GINVLGLIVF CLVFGLVIGK MGEKGQILVD FF NALSDAT MKIVQIIMCY MPLGILFLIA GKIIEVEDWE IFRKLGLYMA TVLTGLAIHS IVILPLIYFI VVRKNPFRFA MGM AQALLT ALMISSSSAT LPVTFRCAEE NNQVDKRITR FVLPVGATIN MDGTALYEAV AAVFIAQLND LDLGIGQIIT ISIT ATSAS IGAAGVPQAG LVTMVIVLSA VGLPAEDVTL IIAVDWLLDR FRTMVNVLGD AFGTGIVEKL SKKELEQMDV SSEVN AENL YFQ

UniProtKB: Excitatory amino acid transporter 3

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Macromolecule #2: B11 nanobody

MacromoleculeName: B11 nanobody / type: protein_or_peptide / ID: 2 / Details: Missing regions are unresolved / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vicugna pacos (alpaca)
Molecular weightTheoretical: 18.429158 KDa
Recombinant expressionOrganism: Escherichia coli MC1061 (bacteria)
SequenceString:
SQGQLVESGG GLVQAGGSLR LSCAASGRPA SMYSMGWFRQ APGKDREFVA AISRYSGSST YYADSVKGRF TISRSNAKNM AFLQMNSLK PEDTAVYYCA ARAGFASDWG THGSDYWGKG TRVTVSALEV LFQGPDYKDH DGDYKDHDID YKDDDDKHHH H HHHHHH

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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

Concentration2 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
150.0 mMNaClsodium chloride
0.003 %C47H88O22Lauryl Maltose Neopentyl Glycol
0.0003 %C31H50O4Cholesteryl hemisuccinate

Details: 20 mM HEPES pH 7.5, 150 mM NaCl, 0.003% LMNG, 0.0003% CHS
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
DetailsObjective aperture 100 um; data collected on eBIC-Diamond Krios III microscope
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 3056 / Average exposure time: 8.32 sec. / Average electron dose: 38.55 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 3.3.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab-initio model from cryoSPARC
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Number images used: 132709
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC (ver. 3.3.1)
Details: Heterogeneous refinement produced 4 classes with 12%, 46%, 33% and 9% particles respectively. The final reconstruction derived from the 46% particle class.
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

6s3q

chain_id: A, source_name: PDB, initial_model_type: experimental model

1zvh

chain_id: B, source_name: PDB, initial_model_type: experimental model
Detailsinitial model fitted with 6S3Q for EAAT3 and 1ZVH for B11 nanobody in COOT. Model was refined in Phenix.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: real space refinement
Output model

PDB-31ic:
Structure of human excitatory amino acid transporter 3 (EAAT3) in complex with B11 nanobody

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