4JTA

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.210 

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Ligand Structure Quality Assessment 


This is version 2.0 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:  
    4JTA, 4JTC, 4JTD

  • 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 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 ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Voltage-gated potassium channel subunit beta-2A, C [auth P]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
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Potassium voltage-gated channel subfamily A member 2, Potassium voltage-gated channel subfamily B member 1B, D [auth Q]514Rattus norvegicusMutation(s): 5 
Gene Names: Kcna2Kcnb1
Membrane Entity: Yes 
UniProt
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 LengthOrganismDetailsImage
Potassium channel toxin alpha-KTx 1.1E [auth Y]37Leiurus quinquestriatus hebraeusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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 (Subject of Investigation/LOI)
Query on PGW

Download Ideal Coordinates CCD File 
DA [auth Q] , J [auth B] , K [auth B] , L [auth B] , M [auth B] , N [auth B] , O [auth B] , P [auth B] , 
DA [auth Q],  J [auth B],  K [auth B],  L [auth B],  M [auth B],  N [auth B],  O [auth B],  P [auth B],  Q [auth B],  R [auth B],  S [auth B],  T [auth B],  U [auth B],  V [auth B],  W [auth B],  X [auth B],  Y [auth B]
(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 (Subject of Investigation/LOI)
Query on NAP

Download Ideal Coordinates CCD File 
F [auth A], Z [auth P]NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
AA [auth Q], BA [auth Q], CA [auth Q], G [auth B], H [auth B], I [auth B]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
E [auth Y]L-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.210 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.4α = 90
b = 144.4β = 90
c = 284.103γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-06-12
    Type: Initial release
  • Version 1.1: 2013-06-19
    Changes: Derived calculations
  • Version 1.2: 2017-08-16
    Changes: Source and taxonomy
  • Version 1.3: 2017-11-15
    Changes: Refinement description
  • Version 2.0: 2019-12-25
    Changes: Database references, Derived calculations, Polymer sequence