6WZB | pdb_00006wzb

Crystal structure of the GltPh V216C-G388C mutant cross-linked with divalent mercury

• PDB DOI: https://doi.org/10.2210/pdb6WZB/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Pyrococcus horikoshii OT3
• Expression System: Escherichia coli
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2020-05-13 Released: 2021-02-17 
• Deposition Author(s): Chen, I., Font, J., Ryan, R.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.45 Å
• R-Value Free: 
  0.268 (Depositor), 0.272 (DCC) 
• R-Value Work: 
  0.233 (Depositor), 0.238 (DCC) 
• R-Value Observed: 
  0.234 (Depositor) 

Starting Model: experimental

Literature

Glutamate transporters have a chloride channel with two hydrophobic gates.

Chen, I., Pant, S., Wu, Q., Cater, R.J., Sobti, M., Vandenberg, R.J., Stewart, A.G., Tajkhorshid, E., Font, J., Ryan, R.M.

(2021) Nature 591: 327-331

• PubMed: 33597752 
• DOI: https://doi.org/10.1038/s41586-021-03240-9
• Primary Citation Related Structures: 
  6WYJ, 6WYK, 6WYL, 6WZB, 6X01


• PubMed Abstract: 
  

  Glutamate is the most abundant excitatory neurotransmitter in the central nervous system, and its precise control is vital to maintain normal brain function and to prevent excitotoxicity ¹ . The removal of extracellular glutamate is achieved by plasma-membrane-bound transporters, which couple glutamate transport to sodium, potassium and pH gradients using an elevator mechanism ^2-5 . Glutamate transporters also conduct chloride ions by means of a channel-like process that is thermodynamically uncoupled from transport ^6-8 . However, the molecular mechanisms that enable these dual-function transporters to carry out two seemingly contradictory roles are unknown. Here we report the cryo-electron microscopy structure of a glutamate transporter homologue in an open-channel state, which reveals an aqueous cavity that is formed during the glutamate transport cycle. The functional properties of this cavity, combined with molecular dynamics simulations, reveal it to be an aqueous-accessible chloride permeation pathway that is gated by two hydrophobic regions and is conserved across mammalian and archaeal glutamate transporters. Our findings provide insight into the mechanism by which glutamate transporters support their dual function, and add information that will assist in mapping the complete transport cycle shared by the solute carrier 1A transporter family.

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Organizational Affiliation: 
• Transporter Biology Group, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia.
NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA.
Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia.
St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Kensington, New South Wales, Australia.
NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA. [e-mail].
Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA. [e-mail].
Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA. [e-mail].
Transporter Biology Group, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia. [e-mail].
Transporter Biology Group, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 134.94 kDa 
• Atom Count: 9,144 
• Modeled Residue Count: 1,233 
• Deposited Residue Count: 1,266 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate transporter homolog	A, B, C	422	Pyrococcus horikoshii OT3	Mutation(s): 3  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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HG	G [auth A], K [auth B], O [auth C]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N
ASP	D [auth A], H [auth B], L [auth C]	ASPARTIC ACID C4 H7 N O4 CKLJMWTZIZZHCS-REOHCLBHSA-N
NA	E [auth A], F [auth A], I [auth B], J [auth B], M [auth C], N [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.45 Å
• R-Value Free:  0.268 (Depositor), 0.272 (DCC) 
• R-Value Work:  0.233 (Depositor), 0.238 (DCC) 
• R-Value Observed: 0.234 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.111	α = 90
b = 204.573	β = 90
c = 207.372	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
Auto-Rickshaw	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-02-17 
Deposition Author(s): Chen, I., Font, J., Ryan, R.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	APP1164494

Revision History  

• Version 1.0: 2021-02-17
  Type: Initial release
  
• Version 1.1: 2021-03-03
  Changes: Database references
• Version 1.2: 2021-03-24
  Changes: Database references
• Version 1.3: 2023-10-18
  Changes: Data collection, Database references, Refinement description