4JTA

Crystal structure of Kv1.2-2.1 paddle chimera channel in complex with Charybdotoxin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of a pore-blocking toxin in complex with a eukaryotic voltage-dependent K(+) channel.

Banerjee, A.Lee, A.Campbell, E.Mackinnon, R.

(2013) Elife 2: e00594-e00594

  • DOI: 10.7554/eLife.00594
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Pore-blocking toxins inhibit voltage-dependent K(+) channels (Kv channels) by plugging the ion-conduction pathway. We have solved the crystal structure of paddle chimera, a Kv channel in complex with charybdotoxin (CTX), a pore-blocking toxin. The to ...

    Pore-blocking toxins inhibit voltage-dependent K(+) channels (Kv channels) by plugging the ion-conduction pathway. We have solved the crystal structure of paddle chimera, a Kv channel in complex with charybdotoxin (CTX), a pore-blocking toxin. The toxin binds to the extracellular pore entryway without producing discernable alteration of the selectivity filter structure and is oriented to project its Lys27 into the pore. The most extracellular K(+) binding site (S1) is devoid of K(+) electron-density when wild-type CTX is bound, but K(+) density is present to some extent in a Lys27Met mutant. In crystals with Cs(+) replacing K(+), S1 electron-density is present even in the presence of Lys27, a finding compatible with the differential effects of Cs(+) vs K(+) on CTX affinity for the channel. Together, these results show that CTX binds to a K(+) channel in a lock and key manner and interacts directly with conducting ions inside the selectivity filter. DOI:http://dx.doi.org/10.7554/eLife.00594.001.


    Organizational Affiliation

    Laboratory of Molecular Neurobiology and Biophysics , Rockefeller University , New York , United States ; Howard Hughes Medical Institute, Rockefeller University , New York , United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Voltage-gated potassium channel subunit beta-2
A, P
333Rattus norvegicusMutation(s): 0 
Gene Names: Kcnab2 (Ckbeta2, Kcnb3)
EC: 1.1.1.-
Find proteins for P62483 (Rattus norvegicus)
Go to UniProtKB:  P62483
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Potassium voltage-gated channel subfamily A member 2, Potassium voltage-gated channel subfamily B member 1
B, Q
514Rattus norvegicusMutation(s): 5 
Gene Names: Kcna2, Kcnb1
Find proteins for P63142 (Rattus norvegicus)
Go to UniProtKB:  P63142
Find proteins for P15387 (Rattus norvegicus)
Go to UniProtKB:  P15387
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Potassium channel toxin alpha-KTx 1.1
Y
37Leiurus quinquestriatus hebraeusMutation(s): 0 
Find proteins for P13487 (Leiurus quinquestriatus hebraeus)
Go to UniProtKB:  P13487
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
B, Q
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
NAP
Query on NAP

Download SDF File 
Download CCD File 
A, P
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
PGW
Query on PGW

Download SDF File 
Download CCD File 
B, Q
(1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
1-Palmitoyl-2-Oleoyl-sn-Glycero-3-[Phospho-(1-glycerol)]; PHOSPHATIDYLGLYCEROL
C40 H77 O10 P
PAZGBAOHGQRCBP-HGWHEPCSSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
Y
L-PEPTIDE LINKINGC5 H7 N O3GLU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.210 
  • Space Group: P 4 21 2
Unit Cell:
Length (Å)Angle (°)
a = 144.400α = 90.00
b = 144.400β = 90.00
c = 284.103γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
HKL-2000data collection
CNSrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-06-12
    Type: Initial release
  • Version 1.1: 2013-06-19
    Type: Derived calculations
  • Version 1.2: 2017-08-16
    Type: Source and taxonomy
  • Version 1.3: 2017-11-15
    Type: Refinement description