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- EMDB-44527: Ancestral uncoupled aspartate transporter, apo conditions, high-a... -

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Basic information

Entry
Database: EMDB / ID: EMD-44527
TitleAncestral uncoupled aspartate transporter, apo conditions, high-affinity state
Map dataApo AncInt, high-affinity (sharpened with DeepEMhancer)
Sample
  • Complex: Ancestral uncoupled aspartate transporter, apo conditions, high-affinity state
    • Protein or peptide: Aspartate transporter
KeywordsTransporter / ion-uncoupled / ancestral / TRANSPORT PROTEIN
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsReddy KD / Boudker O
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R37NS134865 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)F32NS102325 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: bioRxiv / Year: 2024
Title: Evolutionary analysis reveals the origin of sodium coupling in glutamate transporters.
Authors: Krishna D Reddy / Burha Rasool / Farideh Badichi Akher / Nemanja Kutlešić / Swati Pant / Olga Boudker /
Abstract: Secondary active membrane transporters harness the energy of ion gradients to concentrate their substrates. Homologous transporters evolved to couple transport to different ions in response to ...Secondary active membrane transporters harness the energy of ion gradients to concentrate their substrates. Homologous transporters evolved to couple transport to different ions in response to changing environments and needs. The bases of such diversification, and thus principles of ion coupling, are unexplored. Employing phylogenetics and ancestral protein reconstruction, we investigated sodium-coupled transport in prokaryotic glutamate transporters, a mechanism ubiquitous across life domains and critical to neurotransmitter recycling in humans. We found that the evolutionary transition from sodium-dependent to independent substrate binding to the transporter preceded changes in the coupling mechanism. Structural and functional experiments suggest that the transition entailed allosteric mutations, making sodium binding dispensable without affecting ion-binding sites. Allosteric tuning of transporters' energy landscapes might be a widespread route of their functional diversification.
History
DepositionApr 19, 2024-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44527.png

Downloads & links

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Map

FileDownload / File: emd_44527.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationApo AncInt, high-affinity (sharpened with DeepEMhancer)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 297. Å		0.83 Å/pix.
x 360 pix.
= 297. Å		0.83 Å/pix.
x 360 pix.
= 297. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.305
Minimum - Maximum-0.0006157932 - 2.204441
Average (Standard dev.)0.0005494758 (±0.019064024)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 297.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Apo AncInt, high-affinity (half-map 2)

Fileemd_44527_half_map_1.map
AnnotationApo AncInt, high-affinity (half-map 2)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Apo AncInt, high-affinity (half-map 2)

Fileemd_44527_half_map_2.map
AnnotationApo AncInt, high-affinity (half-map 2)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ancestral uncoupled aspartate transporter, apo conditions, high-a...

EntireName: Ancestral uncoupled aspartate transporter, apo conditions, high-affinity state
Components
  • Complex: Ancestral uncoupled aspartate transporter, apo conditions, high-affinity state
    • Protein or peptide: Aspartate transporter

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Supramolecule #1: Ancestral uncoupled aspartate transporter, apo conditions, high-a...

SupramoleculeName: Ancestral uncoupled aspartate transporter, apo conditions, high-affinity state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: Aspartate transporter

MacromoleculeName: Aspartate transporter / type: protein_or_peptide / ID: 1 / Details: apo conditions, high-affinity state / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 43.910488 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSLYHKILIG FVLGVIVGLI FGDKAEFIKP LGDIFLRLLK MIVVPLVFST IVTGIASMGD VKKLGRIGAK TLIYYMITTT LAVTIGLIL ANIFKPGKGL SLGEIHEVAH PNAPSFTETL LNMIPTNPFE AMAEGNMLQI IVFAIFFGIA LALMGEKAEP V KKFFDSAS ...String:
MSLYHKILIG FVLGVIVGLI FGDKAEFIKP LGDIFLRLLK MIVVPLVFST IVTGIASMGD VKKLGRIGAK TLIYYMITTT LAVTIGLIL ANIFKPGKGL SLGEIHEVAH PNAPSFTETL LNMIPTNPFE AMAEGNMLQI IVFAIFFGIA LALMGEKAEP V KKFFDSAS EVMFKITDIV MKFAPYGVFA LMAWTVGKYG LDVLAPLGKL ILTVYLGCII HILIVYTLLL RFLCKINPLR FF KKIKEAM LVAFSTCSSA ATLPVTMRVA EELGVPESIA SFTLPLGATI NMDGTALYQG VAAIFVAQAY GVELTLGQQL TIV LTAVLA SIGTAGVPGA GLVMLTMVLT SVGLPLEGIA LIAGIDRILD MARTTVNVTG DLVATAIVAR TENELNREMT ATPL EVLES KTIAL

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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

BufferpH: 7.4 / Details: 20 mM HEPES, 100 mM NMDG-Cl
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.29 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 63865
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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