4HYO

Crystal Structure of MthK Pore


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 

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

The voltage-dependent gate in MthK potassium channels is located at the selectivity filter.

Posson, D.J.McCoy, J.G.Nimigean, C.M.

(2013) Nat Struct Mol Biol 20: 159-166

  • DOI: https://doi.org/10.1038/nsmb.2473
  • Primary Citation of Related Structures:  
    4HYO, 4HZ3

  • PubMed Abstract: 

    Understanding how ion channels open and close their pores is crucial for comprehending their physiological roles. We used intracellular quaternary ammonium blockers, electrophysiology and X-ray crystallography to locate the voltage-dependent gate in MthK potassium channels from Methanobacterium thermoautotrophicum. Blockers bind in an aqueous cavity between two putative gates: an intracellular gate and the selectivity filter. Thus, these blockers directly probe gate location--an intracellular gate will prevent binding when closed, whereas a selectivity filter gate will always allow binding. Kinetic analysis of tetrabutylammonium block of single MthK channels combined with X-ray crystallographic analysis of the pore with tetrabutyl antimony unequivocally determined that the voltage-dependent gate, like the C-type inactivation gate in eukaryotic channels, is located at the selectivity filter. State-dependent binding kinetics suggest that MthK inactivation leads to conformational changes within the cavity and intracellular pore entrance.


  • Organizational Affiliation

    Department of Anesthesiology, Weill Cornell Medical College, New York, New York, USA. djp2003@med.cornell.edu


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Calcium-gated potassium channel mthK
A, B, C, D, E
A, B, C, D, E, F, G, H
91Methanothermobacter thermautotrophicus str. Delta HMutation(s): 2 
Gene Names: mthKMTH_1520
Membrane Entity: Yes 
UniProt
Find proteins for O27564 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H))
Explore O27564 
Go to UniProtKB:  O27564
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO27564
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEZ
Query on HEZ

Download Ideal Coordinates CCD File 
AA [auth G]
BA [auth H]
M [auth A]
N [auth A]
O [auth B]
AA [auth G],
BA [auth H],
M [auth A],
N [auth A],
O [auth B],
P [auth B],
Q [auth C],
R [auth C],
S [auth D],
T [auth D],
Y [auth E],
Z [auth F]
HEXANE-1,6-DIOL
C6 H14 O2
XXMIOPMDWAUFGU-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
I [auth A]
J [auth A]
K [auth A]
L [auth A]
U [auth E]
I [auth A],
J [auth A],
K [auth A],
L [auth A],
U [auth E],
V [auth E],
W [auth E],
X [auth E]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.035α = 90.03
b = 63.452β = 89.99
c = 63.477γ = 89.99
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
DENZOdata reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-12-26
    Type: Initial release
  • Version 1.1: 2013-03-06
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description