3LUT

A Structural Model for the Full-length Shaker Potassium Channel Kv1.2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 

  • 2A79 - determined by Long, S.B., Campbell, E.B., MacKinnon, R.  

Literature

Structure of the full-length Shaker potassium channel Kv1.2 by normal-mode-based X-ray crystallographic refinement.

Chen, X.Wang, Q.Ni, F.Ma, J.

(2010) Proc.Natl.Acad.Sci.USA 107: 11352-11357

  • DOI: 10.1073/pnas.1000142107

  • PubMed Abstract: 
  • Voltage-dependent potassium channels (Kv) are homotetramers composed of four voltage sensors and one pore domain. Because of high-level structural flexibility, the first mammalian Kv structure, Kv1.2 at 2.9 A, has about 37% molecular mass of the tran ...

    Voltage-dependent potassium channels (Kv) are homotetramers composed of four voltage sensors and one pore domain. Because of high-level structural flexibility, the first mammalian Kv structure, Kv1.2 at 2.9 A, has about 37% molecular mass of the transmembrane portion not resolved. In this study, by applying a novel normal-mode-based X-ray crystallographic refinement method to the original diffraction data and structural model, we established the structure of full-length Kv1.2 in its native form. This structure offers mechanistic insights into voltage sensing. Particularly, it shows a hydrophobic layer of about 10 A at the midpoint of the membrane bilayer, which is likely the molecular basis for the observed "focused electric field" of Kv1.2 between the internal and external solutions. This work also demonstrated the potential of the refinement method in bringing up large chunks of missing densities, thus beneficial to structural refinement of many difficult systems.


    Related Citations: 
    • Crystal Structure of a Mammalian Voltage-Dependent Shaker Family K+ Channel
      Long, S.B.,Campbell, E.B.,MacKinnon, R.
      (2005) Science 309: 897
    • Atomic structure of a voltage-dependent K+ channel inalipidmembrane-like environment
      Long, S.B.,Tao, X.,Campbell, E.B.,Mackinnon, R.
      (2007) Nature 450: 376


    Organizational Affiliation

    Graduate Program of Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Voltage-gated potassium channel subunit beta-2
A
367Rattus norvegicusGene Names: Kcnab2 (Ckbeta2, Kcnb3)
EC: 1.1.1.-
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Potassium, Sodium, & Proton Ion-Selective
Protein: 
Kv1.2 Voltage-gated potassium Channel
Find proteins for P62483 (Rattus norvegicus)
Go to UniProtKB:  P62483
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Potassium voltage-gated channel subfamily A member 2
B
499Rattus norvegicusGene Names: Kcna2
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Potassium, Sodium, & Proton Ion-Selective
Protein: 
Kv1.2 Voltage-gated potassium Channel
Find proteins for P63142 (Rattus norvegicus)
Go to UniProtKB:  P63142
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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

Download SDF File 
Download CCD File 
A
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.211 
  • Space Group: I 4
Unit Cell:
Length (Å)Angle (°)
a = 113.605α = 90.00
b = 113.605β = 90.00
c = 260.473γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
MOLREPphasing
HKL-2000data collection
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-06-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-10-26
    Type: Other