4JTD

Crystal structure of Kv1.2-2.1 paddle chimera channel in complex with Lys27Met mutant of Charybdotoxin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report



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
  • Structures With Same Primary Citation

  • 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-2A, G333Rattus norvegicusMutation(s): 0 
Gene Names: Ckbeta2Kcnab2Kcnb3
EC: 1.1.1
Find proteins for P62483 (Rattus norvegicus)
Explore P62483 
Go to UniProtKB:  P62483
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Potassium voltage-gated channel subfamily A member 2, Potassium voltage-gated channel subfamily B member 1B, H514Rattus norvegicusMutation(s): 5 
Gene Names: Kcna2Kcnb1
Find proteins for P15387 (Rattus norvegicus)
Explore P15387 
Go to UniProtKB:  P15387
Find proteins for P63142 (Rattus norvegicus)
Explore P63142 
Go to UniProtKB:  P63142
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Potassium channel toxin alpha-KTx 1.1Y37Leiurus quinquestriatus hebraeusMutation(s): 1 
Find proteins for P13487 (Leiurus hebraeus)
Explore P13487 
Go to UniProtKB:  P13487
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PGW
Query on PGW

Download CCD File 
B, 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
 Ligand Interaction
NAP
Query on NAP

Download CCD File 
A, G
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
K
Query on K

Download CCD File 
B, H
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
YL-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.210 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.867α = 90
b = 144.867β = 90
c = 284.292γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-06-12
    Type: Initial release
  • Version 1.1: 2017-08-16
    Changes: Source and taxonomy
  • Version 1.2: 2017-11-15
    Changes: Refinement description
  • Version 2.0: 2019-12-25
    Changes: Database references, Derived calculations, Polymer sequence