2HG5

Cs+ complex of a K channel with an amide to ester substitution in the selectivity filter

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.239 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history. 

Literature

Structural and Functional Consequences of an Amide-to-Ester Substitution in the Selectivity Filter of a Potassium Channel.

Valiyaveetil, F.I., Sekedat, M., Mackinnon, R., Muir, T.W.

(2006) J.Am.Chem.Soc. 128: 11591-11599

  • DOI: 10.1021/ja0631955
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • The selectivity filter of K(+) channels comprises four contiguous ion binding sites, S1 through S4. Structural and functional data indicate that the filter contains on average two K(+) ions at any given time and that these ions reside primarily in tw ...

    The selectivity filter of K(+) channels comprises four contiguous ion binding sites, S1 through S4. Structural and functional data indicate that the filter contains on average two K(+) ions at any given time and that these ions reside primarily in two configurations, namely to sites S1 and S3 or to sites S2 and S4. Maximum ion flux through the channel is expected to occur when the energy difference between these two binding configurations is zero. In this study, we have used protein semisynthesis to selectively perturb site 1 within the filter of the KcsA channel through use of an amide-to-ester substitution. The modification alters K(+) conduction properties. The structure of the selectivity filter is largely unperturbed by the modification, despite the loss of an ordered water molecule normally located just behind the filter. Introduction of the ester moiety was found to alter the distribution of K(+), Rb(+,) and Cs(+) within the filter, with the most dramatic change found for Rb(+). The redistribution of ions is associated with the appearance of a partially hydrated ion just external to the filter, at a position where no ion is observed in the wild-type channel. The appearance of this new ion-binding site creates a change in the distance between a pair of K(+) ions some fraction of the time, apparently leading to a reduction in the ion conduction rate. Importantly, this finding suggests that the selectivity filter of a potassium channel is optimized both in terms of absolute ion occupancy and in terms of the separation in distance between the conducting ions.

    Organizational Affiliation: 

    Laboratory of Molecular Neurobiology and Biophysics, The Rockefeller University, New York, New York 10021, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FAB HEAVY CHAIN
A
219Rattus norvegicusMutation(s): 0 
Gene Names: Ighg
Find proteins for Q569B4 (Rattus norvegicus)
Go to UniProtKB:  Q569B4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
FAB LIGHT CHAIN
B
212Mus musculusMutation(s): 0 
Gene Names: Igkc
Find proteins for P01837 (Mus musculus)
Go to UniProtKB:  P01837
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
KCSA CHANNEL
C
57Streptomyces lividansMutation(s): 0 
Gene Names: kcsA (skc1)
Find proteins for P0A334 (Streptomyces lividans)
Go to UniProtKB:  P0A334
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
KCSA CHANNEL
D
43Streptomyces lividansMutation(s): 0 
Gene Names: kcsA (skc1)
Find proteins for P0A334 (Streptomyces lividans)
Go to UniProtKB:  P0A334
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B3H
Query on B3H
Download SDF File 
Download CCD File 
D
(2S)-2-(BUTYRYLOXY)-3-HYDROXYPROPYL NONANOATE
C16 H30 O5
JCEXPOMAGTUEEX-AWEZNQCLSA-N
 Ligand Interaction
GOA
Query on GOA
Download SDF File 
Download CCD File 
C
GLYCOLIC ACID
HYDROXYACETIC ACID; HYDROXYETHANOIC ACID
C2 H4 O3
AEMRFAOFKBGASW-UHFFFAOYSA-N
 Ligand Interaction
CS
Query on CS
Download SDF File 
Download CCD File 
C, D
CESIUM ION
Cs
NCMHKCKGHRPLCM-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.239 
  • Space Group: I 4
Unit Cell:
Length (Å)Angle (°)
a = 156.597α = 90.00
b = 156.597β = 90.00
c = 75.706γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-09-12
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-11-16
    Type: Atomic model
  • Version 1.4: 2017-10-18
    Type: Refinement description