7M2I

Structural Snapshots of Intermediates in the Gating of a K+ Channel


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.231 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structures of Gating Intermediates in a K + channell.

Reddi, R.Matulef, K.Riederer, E.Moenne-Loccoz, P.Valiyaveetil, F.I.

(2021) J Mol Biol 433: 167296-167296

  • DOI: https://doi.org/10.1016/j.jmb.2021.167296
  • Primary Citation of Related Structures:  
    7M2H, 7M2I, 7M2J, 7RP0

  • PubMed Abstract: 

    Regulation of ion conduction through the pore of a K + channel takes place through the coordinated action of the activation gate at the bundle crossing of the inner helices and the inactivation gate located at the selectivity filter. The mechanism of allosteric coupling of these gates is of key interest. Here we report new insights into this allosteric coupling mechanism from studies on a W67F mutant of the KcsA channel. W67 is in the pore helix and is highly conserved in K + channels. The KcsA W67F channel shows severely reduced inactivation and an enhanced rate of activation. We use continuous wave EPR spectroscopy to establish that the KcsA W67F channel shows an altered pH dependence of activation. Structural studies on the W67F channel provide the structures of two intermediate states: a pre- open state and a pre-inactivated state of the KcsA channel. These structures highlight key nodes in the allosteric pathway. The structure of the KcsA W67F channel with the activation gate open shows altered ion occupancy at the second ion binding site (S2) in the selectivity filter. This finding in combination with previous studies strongly support a requirement for ion occupancy at the S2 site for the channel to inactivate.


  • Organizational Affiliation

    Program in Chemical Biology, Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd, Portland, OR 97239, United States. Electronic address: https://twitter.com/Ravi_K_Reddi.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Monoclonal antibody (IgG) against KcsA, Fab heavy chain219Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Monoclonal antibody (IgG) against KcsA, Fab light chain212Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
pH-gated potassium channel KcsA96Streptomyces lividansMutation(s): 0 
Gene Names: kcsAskc1
Membrane Entity: Yes 
UniProt
Find proteins for P0A334 (Streptomyces lividans)
Explore P0A334 
Go to UniProtKB:  P0A334
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A334
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1EM
Query on 1EM

Download Ideal Coordinates CCD File 
E [auth C](1S)-2-HYDROXY-1-[(NONANOYLOXY)METHYL]ETHYL MYRISTATE
C26 H50 O5
IHUWMVGHYXVIRN-DEOSSOPVSA-N
F09
Query on F09

Download Ideal Coordinates CCD File 
D [auth A]NONAN-1-OL
C9 H20 O
ZWRUINPWMLAQRD-UHFFFAOYSA-N
K (Subject of Investigation/LOI)
Query on K

Download Ideal Coordinates CCD File 
F [auth C]
G [auth C]
H [auth C]
I [auth C]
J [auth C]
F [auth C],
G [auth C],
H [auth C],
I [auth C],
J [auth C],
K [auth C]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.231 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 155.25α = 90
b = 155.25β = 90
c = 74.415γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM087546

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-27
    Type: Initial release
  • Version 1.1: 2021-11-10
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary