4GX0 | pdb_00004gx0

Crystal structure of the GsuK L97D mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.249 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.205 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted GLCClick on this verticalbar to view details

This is version 2.1 of the entry. See complete history


Literature

Distinct gating mechanisms revealed by the structures of a multi-ligand gated K(+) channel.

Kong, C.Zeng, W.Ye, S.Chen, L.Sauer, D.B.Lam, Y.Derebe, M.G.Jiang, Y.

(2012) Elife 1: e00184-e00184

  • DOI: https://doi.org/10.7554/eLife.00184
  • Primary Citation of Related Structures:  
    4GVL, 4GX0, 4GX1, 4GX2, 4GX5

  • PubMed Abstract: 

    The gating ring-forming RCK domain regulates channel gating in response to various cellular chemical stimuli in eukaryotic Slo channel families and the majority of ligand-gated prokaryotic K(+) channels and transporters. Here we present structural and functional studies of a dual RCK-containing, multi-ligand gated K(+) channel from Geobacter sulfurreducens, named GsuK. We demonstrate that ADP and NAD(+) activate the GsuK channel, whereas Ca(2+) serves as an allosteric inhibitor. Multiple crystal structures elucidate the structural basis of multi-ligand gating in GsuK, and also reveal a unique ion conduction pore with segmented inner helices. Structural comparison leads us to propose a novel pore opening mechanics that is distinct from other K(+) channels.DOI:http://dx.doi.org/10.7554/eLife.00184.001.


  • Organizational Affiliation

    Department of Physiology , University of Texas Southwestern Medical Center , Dallas , United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TrkA domain protein
A, B, C, D
565Geobacter sulfurreducens PCAMutation(s): 3 
Gene Names: GSU0527
Membrane Entity: Yes 
UniProt
Find proteins for Q74FS9 (Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA))
Explore Q74FS9 
Go to UniProtKB:  Q74FS9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ74FS9
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
E
2N/A
Glycosylation Resources
GlyTouCan:  G07411ON
GlyCosmos:  G07411ON
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GLC
Query on GLC

Download Ideal Coordinates CCD File 
GA [auth D],
S [auth B],
T [auth B]
alpha-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
CA [auth C],
FA [auth D],
M [auth A],
Q [auth B],
R [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN
Query on ZN

Download Ideal Coordinates CCD File 
EA [auth D],
K [auth A],
N [auth B],
Y [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
AA [auth C],
L [auth A],
O [auth B],
Z [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
BA [auth C]
DA [auth D]
F [auth A]
G [auth A]
H [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.249 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.205 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 232.934α = 90
b = 111.67β = 134.47
c = 164.133γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted GLCClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-12-26
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2024-02-28
    Changes: Data collection, Database references, Structure summary