7MHR | pdb_00007mhr

KcsA E71V closed gate with K+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 
    0.203 (Depositor), 0.213 (DCC) 
  • R-Value Work: 
    0.168 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 
    0.169 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

A distinct mechanism of C-type inactivation in the Kv-like KcsA mutant E71V.

Rohaim, A.Vermeulen, B.J.A.Li, J.Kummerer, F.Napoli, F.Blachowicz, L.Medeiros-Silva, J.Roux, B.Weingarth, M.

(2022) Nat Commun 13: 1574-1574

  • DOI: https://doi.org/10.1038/s41467-022-28866-9
  • Primary Citation Related Structures: 
    7MHR, 7MHX, 7MJT, 7MK6, 7MUB

  • PubMed Abstract: 

    C-type inactivation is of great physiological importance in voltage-activated K + channels (Kv), but its structural basis remains unresolved. Knowledge about C-type inactivation has been largely deduced from the bacterial K + channel KcsA, whose selectivity filter constricts under inactivating conditions. However, the filter is highly sensitive to its molecular environment, which is different in Kv channels than in KcsA. In particular, a glutamic acid residue at position 71 along the pore helix in KcsA is substituted by a valine conserved in most Kv channels, suggesting that this side chain is a molecular determinant of function. Here, a combination of X-ray crystallography, solid-state NMR and MD simulations of the E71V KcsA mutant is undertaken to explore inactivation in this Kv-like construct. X-ray and ssNMR data show that the filter of the Kv-like mutant does not constrict under inactivating conditions. Rather, the filter adopts a conformation that is slightly narrowed and rigidified. On the other hand, MD simulations indicate that the constricted conformation can nonetheless be stably established in the mutant channel. Together, these findings suggest that the Kv-like KcsA mutant may be associated with different modes of C-type inactivation, showing that distinct filter environments entail distinct C-type inactivation mechanisms.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, The University of Chicago, 929 E 57th Street, Chicago, IL, 60637, USA.

Macromolecule Content 

  • Total Structure Weight: 60.15 kDa 
  • Atom Count: 4,240 
  • Modeled Residue Count: 534 
  • Deposited Residue Count: 555 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab heavy chain219Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab light chain212Mus musculusMutation(s): 0 
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
pH-gated potassium channel KcsA124Streptomyces lividansMutation(s): 2 
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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free:  0.203 (Depositor), 0.213 (DCC) 
  • R-Value Work:  0.168 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 0.169 (Depositor) 
Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 155.832α = 90
b = 155.832β = 90
c = 76.255γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHASERphasing

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 States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-23
    Type: Initial release
  • Version 1.1: 2022-04-06
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-10-09
    Changes: Structure summary