2HMT

Diamond-shaped octameric ring structure of an RCK domain with NADH bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The RCK Domain of the KtrAB K(+) Transporter: Multiple Conformations of an Octameric Ring.

Albright, R.A.Ibar, J.L.Kim, C.U.Gruner, S.M.Morais-Cabral, J.H.

(2006) Cell 126: 1147-1159

  • DOI: 10.1016/j.cell.2006.08.028
  • Primary Citation of Related Structures:  2HMS, 2HMU, 2HMV, 2HMW

  • PubMed Abstract: 
  • The KtrAB ion transporter is a complex of the KtrB membrane protein and KtrA, an RCK domain. RCK domains regulate eukaryotic and prokaryotic membrane proteins involved in K(+) transport. Conflicting functional models have proposed two different oligo ...

    The KtrAB ion transporter is a complex of the KtrB membrane protein and KtrA, an RCK domain. RCK domains regulate eukaryotic and prokaryotic membrane proteins involved in K(+) transport. Conflicting functional models have proposed two different oligomeric arrangements for RCK domains, tetramer versus octamer. Our results for the KtrAB RCK domain clearly show an octamer in solution and in the crystal. We determined the structure of this protein in three different octameric ring conformations that resemble the RCK-domain octamer observed in the MthK potassium channel but show striking differences in size and symmetry. We present experimental evidence for the association between one RCK octameric ring and two KtrB membrane proteins. These results provide insights into the quaternary organization of the KtrAB transporter and its mechanism of activation and show that the RCK-domain octameric ring model is generally applicable to other ion-transport systems.


    Related Citations: 
    • A Mechanism of Regulating Transmembrane Potassium Flux through a Ligand-Mediated Conformational Switch
      Roosild, T.P.,Miller, S.,Booth, I.R.,Choe, S.
      (2002) Cell 109: 781
    • Crystal structure and mechanism of a calcium-gated potassium channel
      Jiang, Y.,Lee, A.,Chen, J.,Cadene, M.,Chait, B.T.,MacKinnon, R.
      (2002) Nature 417: 501


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
YuaA protein
A, B
144Bacillus subtilis (strain 168)Gene Names: ktrA (yuaA)
Find proteins for O32080 (Bacillus subtilis (strain 168))
Go to UniProtKB:  O32080
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAI
Query on NAI

Download SDF File 
Download CCD File 
A, B
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
NADH
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.232 
  • Space Group: P 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 127.405α = 90.00
b = 127.405β = 90.00
c = 50.867γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
MOLREPphasing
PDB_EXTRACTdata extraction
HKL-2000data reduction
DENZOdata reduction
HKL-2000data scaling
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-09-26
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description