2KSF

Backbone structure of the membrane domain of E. coli histidine kinase receptor KdpD, Center for Structures of Membrane Proteins (CSMP) target 4312C


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Membrane domain structures of three classes of histidine kinase receptors by cell-free expression and rapid NMR analysis.

Maslennikov, I.Klammt, C.Hwang, E.Kefala, G.Okamura, M.Esquivies, L.Mors, K.Glaubitz, C.Kwiatkowski, W.Jeon, Y.H.Choe, S.

(2010) Proc.Natl.Acad.Sci.USA 107: 10902-10907

  • DOI: 10.1073/pnas.1001656107
  • Primary Citation of Related Structures:  2KSE, 2KSD

  • PubMed Abstract: 
  • NMR structural studies of membrane proteins (MP) are hampered by complications in MP expression, technical difficulties associated with the slow process of NMR spectral peak assignment, and limited distance information obtainable for transmembrane (T ...

    NMR structural studies of membrane proteins (MP) are hampered by complications in MP expression, technical difficulties associated with the slow process of NMR spectral peak assignment, and limited distance information obtainable for transmembrane (TM) helices. To overcome the inherent challenges in the determination of MP structures, we have developed a rapid and cost-efficient strategy that combines cell-free (CF) protein synthesis, optimized combinatorial dual-isotope labeling for nearly instant resonance assignment, and fast acquisition of long-distance information using paramagnetic probes. Here we report three backbone structures for the TM domains of the three classes of Escherichia coli histidine kinase receptors (HKRs). The ArcB and QseC TM domains are both two-helical motifs, whereas the KdpD TM domain comprises a four-helical bundle with shorter second and third helices. The interhelical distances (up to 12 A) reveal weak interactions within the TM domains of all three receptors. Determined consecutively within 8 months, these structures offer insight into the abundant and underrepresented in the Protein Data Bank class of 2-4 TM crossers and demonstrate the efficiency of our CF combinatorial dual-labeling strategy, which can be applied to solve MP structures in high numbers and at a high speed. Our results greatly expand the current knowledge of HKR structure, opening the doors to studies on their widespread and pharmaceutically important bacterial signaling mechanism.


    Organizational Affiliation

    Structural Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sensor protein kdpD
A
107Escherichia coli (strain K12)Gene Names: kdpD
EC: 2.7.13.3
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Histidine Kinase Receptors
Protein: 
KdpD (397-502) Sensor protein membrane domain
Find proteins for P21865 (Escherichia coli (strain K12))
Go to UniProtKB:  P21865
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 
  • Olderado: 2KSF Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-03-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-12-05
    Type: Database references