3LNM

F233W mutant of the Kv2.1 paddle-Kv1.2 chimera channel


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.211 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

A gating charge transfer center in voltage sensors.

Tao, X.Lee, A.Limapichat, W.Dougherty, D.A.MacKinnon, R.

(2010) Science 328: 67-73

  • DOI: https://doi.org/10.1126/science.1185954
  • Primary Citation of Related Structures:  
    3LNM

  • PubMed Abstract: 

    Voltage sensors regulate the conformations of voltage-dependent ion channels and enzymes. Their nearly switchlike response as a function of membrane voltage comes from the movement of positively charged amino acids, arginine or lysine, across the membrane field. We used mutations with natural and unnatural amino acids, electrophysiological recordings, and x-ray crystallography to identify a charge transfer center in voltage sensors that facilitates this movement. This center consists of a rigid cyclic "cap" and two negatively charged amino acids to interact with a positive charge. Specific mutations induce a preference for lysine relative to arginine. By placing lysine at specific locations, the voltage sensor can be stabilized in different conformations, which enables a dissection of voltage sensor movements and their relation to ion channel opening.


  • Organizational Affiliation

    Laboratory of Molecular Neurobiology and Biophysics, Rockefeller University, Howard Hughes Medical Institute, 1230 York Avenue, New York, NY 10065, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Voltage-gated potassium channel subunit beta-2
A, C
333Rattus norvegicusMutation(s): 0 
Gene Names: Ckbeta2Kcnab2Kcnb3
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
F233W mutant of the Kv2.1 paddle-Kv1.2 chimera
B, D
514Rattus norvegicusMutation(s): 6 
Gene Names: Kcna2
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP63142P15387
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],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
X [auth D]
(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],
W [auth C]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
K
Query on K

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
CA [auth D]
R [auth B]
S [auth B]
AA [auth D],
BA [auth D],
CA [auth D],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
Y [auth D],
Z [auth D]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.211 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.271α = 90
b = 144.271β = 90
c = 284.06γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
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: 2010-04-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-08-02
    Changes: Refinement description, Source and taxonomy
  • Version 1.3: 2021-10-13
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-09-06
    Changes: Data collection, Refinement description