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- PDB-9bh0: Ancestral uncoupled aspartate transporter in complex with L-aspartate -

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Basic information

Entry
Database: PDB / ID: 9bh0
TitleAncestral uncoupled aspartate transporter in complex with L-aspartate
ComponentsAspartate transporter
KeywordsTRANSPORT PROTEIN / Transporter / ion-uncoupled / ancestral
Function / homologyASPARTIC ACID
Function and homology information
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsReddy, K.D. / Boudker, O.
Funding support United States, 2items
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
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, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
A: Aspartate transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0442
Polymers43,9101
Non-polymers1331
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Aspartate transporter


Mass: 43910.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C-terminal thrombin cleavage site, Twin-Strep tag, ALFA tag, and (HIS)10 tag. Engineered with loops and tails from NCBI KJS87745.1
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7NO4 / Feature type: SUBJECT OF INVESTIGATION
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: Ancestral uncoupled aspartate transporter in complex with L-aspartate
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Pyrococcus horikoshii (archaea)
Source (recombinant)Organism: Escherichia coli str. K-12 substr. DH10B (bacteria)
Buffer solutionpH: 7.4 / Details: 20 mM HEPES, 100 mM NMDG-Cl, 1 mM L-Asp
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: 2100 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 58 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 71731 / Symmetry type: POINT

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