9BH2 | pdb_00009bh2

Apo GltPh, outward-facing state

• PDB DOI: https://doi.org/10.2210/pdb9BH2/pdb
• EM Map EMD-44530: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Pyrococcus horikoshii
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  PDBTM


• Deposited: 2024-04-19 Released: 2025-03-12 
• Deposition Author(s): Reddy, K.D., Boudker, O.
• Funding Organization(s): National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS), Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Evolutionary analysis reveals the origin of sodium coupling in glutamate transporters.

Reddy, K.D., Rasool, B., Akher, F.B., Kutlesic, N., Pant, S., Boudker, O.

(2024) bioRxiv 

• PubMed: 38106174 
• DOI: https://doi.org/10.1101/2023.12.03.569786
• Primary Citation Related Structures: 
  9BGY, 9BGZ, 9BH0, 9BH1, 9BH2


• PubMed 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 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.

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Organizational Affiliation: 
• Dept. of Physiology & Biophysics, Weill Cornell Medical College, 1300 York Ave, New York, NY 10021, USA.
Dept. of Biochemistry, Weill Cornell Medical College, 1300 York Ave, New York, NY 10021, USA.
Howard Hughes Medical Institute, Weill Cornell Medical College, 1300 York Ave, New York, NY 10021, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 44.64 kDa 
• Atom Count: 3,078 
• Modeled Residue Count: 414 
• Deposited Residue Count: 422 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate transporter homolog	A	422	Pyrococcus horikoshii	Mutation(s): 0  Gene Names: PH1295 Membrane Entity: Yes
UniProt
Find proteins for O59010 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O59010  Go to UniProtKB:  O59010

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-03-12 
Deposition Author(s): Reddy, K.D., Boudker, O.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	F32NS102325
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	R37NS134865
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2025-03-12
  Type: Initial release