3KBC | pdb_00003kbc

Crystal structure of GltPh K55C-A364C mutant crosslinked with divalent mercury


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.51 Å
  • R-Value Free: 
    0.270 (Depositor), 0.299 (DCC) 
  • R-Value Work: 
    0.267 (Depositor) 
  • R-Value Observed: 
    0.267 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 3KBC

This is version 1.3 of the entry. See complete history

Literature

Transport mechanism of a bacterial homologue of glutamate transporters.

Reyes, N.Ginter, C.Boudker, O.

(2009) Nature 462: 880-885

  • DOI: https://doi.org/10.1038/nature08616
  • Primary Citation Related Structures: 
    3KBC

  • PubMed Abstract: 

    Glutamate transporters are integral membrane proteins that catalyse a thermodynamically uphill uptake of the neurotransmitter glutamate from the synaptic cleft into the cytoplasm of glia and neuronal cells by harnessing the energy of pre-existing electrochemical gradients of ions. Crucial to the reaction is the conformational transition of the transporters between outward and inward facing states, in which the substrate binding sites are accessible from the extracellular space and the cytoplasm, respectively. Here we describe the crystal structure of a double cysteine mutant of a glutamate transporter homologue from Pyrococcus horikoshii, Glt(Ph), which is trapped in the inward facing state by cysteine crosslinking. Together with the previously determined crystal structures of Glt(Ph) in the outward facing state, the structure of the crosslinked mutant allows us to propose a molecular mechanism by which Glt(Ph) and, by analogy, mammalian glutamate transporters mediate sodium-coupled substrate uptake.


  • Organizational Affiliation
    • Department of Physiology and Biophysics, Weill Cornell Medical College, 1300 York Avenue, Box 75, New York, New York 10065, USA.

Macromolecule Content 

  • Total Structure Weight: 135.81 kDa 
  • Atom Count: 9,096 
  • Modeled Residue Count: 1,233 
  • Deposited Residue Count: 1,275 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
425aa long hypothetical proton glutamate symport protein
A, B, C
425Pyrococcus horikoshiiMutation(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
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HG

Query on HG



Download:Ideal Coordinates CCD File
E [auth A],
I [auth B],
M [auth C]
MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
ASP

Query on ASP



Download:Ideal Coordinates CCD File
D [auth A],
H [auth B],
L [auth C]
ASPARTIC ACID
C4 H7 N O4
CKLJMWTZIZZHCS-REOHCLBHSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
J [auth B]
K [auth B]
N [auth C]
F [auth A],
G [auth A],
J [auth B],
K [auth B],
N [auth C],
O [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.51 Å
  • R-Value Free:  0.270 (Depositor), 0.299 (DCC) 
  • R-Value Work:  0.267 (Depositor) 
  • R-Value Observed: 0.267 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.142α = 90
b = 206.78β = 90
c = 205.971γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-12-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2021-10-13
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-09-06
    Changes: Data collection, Refinement description