5WIE

Crystal structure of a Kv1.2-2.1 chimera K+ channel V406W mutant in an inactivated state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.236 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Crystal structure of an inactivated mutant mammalian voltage-gated K(+) channel.

Pau, V.Zhou, Y.Ramu, Y.Xu, Y.Lu, Z.

(2017) Nat Struct Mol Biol 24: 857-865

  • DOI: https://doi.org/10.1038/nsmb.3457
  • Primary Citation of Related Structures:  
    5WIE

  • PubMed Abstract: 

    C-type inactivation underlies important roles played by voltage-gated K + (Kv) channels. Functional studies have provided strong evidence that a common underlying cause of this type of inactivation is an alteration near the extracellular end of the channel's ion-selectivity filter. Unlike N-type inactivation, which is known to reflect occlusion of the channel's intracellular end, the structural mechanism of C-type inactivation remains controversial and may have many detailed variations. Here we report that in voltage-gated Shaker K + channels lacking N-type inactivation, a mutation enhancing inactivation disrupts the outermost K + site in the selectivity filter. Furthermore, in a crystal structure of the Kv1.2-2.1 chimeric channel bearing the same mutation, the outermost K + site, which is formed by eight carbonyl-oxygen atoms, appears to be slightly too small to readily accommodate a K + ion and in fact exhibits little ion density; this structural finding is consistent with the functional hallmark of C-type inactivation.


  • Organizational Affiliation

    Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Voltage-gated potassium channel subunit beta-2A,
C [auth G]
333Rattus norvegicusMutation(s): 0 
Gene Names: Kcnab2Ckbeta2Kcnb3
EC: 1.1.1
Membrane Entity: Yes 
UniProt
Find proteins for P62483 (Rattus norvegicus)
Explore P62483 
Go to UniProtKB:  P62483
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62483
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Potassium voltage-gated channel subfamily A member 2,Potassium voltage-gated channel subfamily A member 2B,
D [auth H]
532Rattus norvegicusMus musculus
This entity is chimeric
Mutation(s): 1 
Gene Names: Kcna2
Membrane Entity: Yes 
UniProt
Find proteins for P63142 (Rattus norvegicus)
Explore P63142 
Go to UniProtKB:  P63142
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63142
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PGW
Query on PGW

Download Ideal Coordinates CCD File 
F [auth B]
G [auth B]
H [auth B]
I [auth B]
J [auth B]
F [auth B],
G [auth B],
H [auth B],
I [auth B],
J [auth B],
P [auth H]
(1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
C40 H77 O10 P
PAZGBAOHGQRCBP-HGWHEPCSSA-N
NAP
Query on NAP

Download Ideal Coordinates CCD File 
E [auth A],
O [auth G]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
K
Query on K

Download Ideal Coordinates CCD File 
K [auth B]
L [auth B]
M [auth B]
N [auth B]
Q [auth H]
K [auth B],
L [auth B],
M [auth B],
N [auth B],
Q [auth H],
R [auth H],
S [auth H],
T [auth H]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.236 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.124α = 90
b = 143.124β = 90
c = 284.51γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM055560
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesRO1DK109919

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-30
    Type: Initial release
  • Version 1.1: 2017-09-13
    Changes: Database references
  • Version 1.2: 2017-09-27
    Changes: Author supporting evidence
  • Version 1.3: 2017-10-18
    Changes: Database references
  • Version 1.4: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.5: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description