4IZM

Crystal structure of GltPh L66C-S300C mutant crosslinked with divalent mercury


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.50 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.253 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Binding thermodynamics of a glutamate transporter homolog.

Reyes, N.Oh, S.Boudker, O.

(2013) Nat Struct Mol Biol 20: 634-640

  • DOI: https://doi.org/10.1038/nsmb.2548
  • Primary Citation of Related Structures:  
    4IZM

  • PubMed Abstract: 

    Glutamate transporters catalyze concentrative uptake of the neurotransmitter into glial cells and neurons. Their transport cycle involves binding and release of the substrate on the extra- and intracellular sides of the plasma membranes and translocation of the substrate-binding site across the lipid bilayers. The energy of the ionic gradients, mainly sodium, fuels the cycle. Here, we used a cross-linking approach to trap a glutamate transporter homolog from Pyrococcus horikoshii in key conformational states with the substrate-binding site facing either the extracellular or the intracellular side of the membrane to study binding thermodynamics. We show that the chemical potential of sodium ions in solution is exclusively coupled to substrate binding and release, not to substrate translocation. Despite the transporter's structural symmetry, the binding mechanisms are distinct on the opposite sides of the membrane and more complex than the current models suggest.


  • Organizational Affiliation

    Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, USA. nicolas.reyes@pasteur.fr


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
425aa long hypothetical proton glutamate symport protein
A, B, C
421Pyrococcus horikoshii OT3Mutation(s): 10 
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO59010
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HG
Query on HG

Download Ideal Coordinates CCD File 
G [auth A],
K [auth B],
O [auth C]
MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
ASP
Query on ASP

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
N [auth C]
ASPARTIC ACID
C4 H7 N O4
CKLJMWTZIZZHCS-REOHCLBHSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
H [auth B]
I [auth B]
L [auth C]
D [auth A],
E [auth A],
H [auth B],
I [auth B],
L [auth C],
M [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
ASP PDBBind:  4IZM Kd: 220 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.50 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.253 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.708α = 90
b = 119.708β = 90
c = 333.72γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-04-10
    Type: Initial release
  • Version 1.1: 2013-06-19
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations