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 

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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 U S A 107: 10902-10907

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

  • 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 (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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sensor protein kdpD107Escherichia coli K-12Mutation(s): 0 
Gene Names: b0695JW0683kdpD
Membrane Entity: Yes 
Find proteins for P21865 (Escherichia coli (strain K12))
Explore P21865 
Go to UniProtKB:  P21865
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21865
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-12-05
    Changes: Database references
  • Version 1.3: 2024-05-01
    Changes: Data collection, Database references