6TNE | pdb_00006tne

Crystal structure of receiver domain from Hybrid Histidine Kinase CckA

• PDB DOI: https://doi.org/10.2210/pdb6TNE/pdb

• Classification: TRANSFERASE
• Organism(s): Caulobacter vibrioides
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-12-06 Released: 2020-12-16 
• Deposition Author(s): Dubey, B.N., Bruederlin, M., Schirmer, T.
• Funding Organization(s): Swiss National Science Foundation

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 
  0.188 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: other

Literature

Structural features discriminating hybrid histidine kinase Rec domains from response regulator homologs.

Bruderlin, M., Bohm, R., Fadel, F., Hiller, S., Schirmer, T., Dubey, B.N.

(2023) Nat Commun 14: 1002-1002

• PubMed: 36864019 
• DOI: https://doi.org/10.1038/s41467-023-36597-8
• Primary Citation of Related Structures:  
  6TNE


• PubMed Abstract: 
  

  In two-component systems, the information gathered by histidine kinases (HKs) are relayed to cognate response regulators (RRs). Thereby, the phosphoryl group of the auto-phosphorylated HK is transferred to the receiver (Rec) domain of the RR to allosterically activate its effector domain. In contrast, multi-step phosphorelays comprise at least one additional Rec (Rec _inter ) domain that is typically part of the HK and acts as an intermediary for phosphoryl-shuttling. While RR Rec domains have been studied extensively, little is known about discriminating features of Rec _inter domains. Here we study the Rec _inter domain of the hybrid HK CckA by X-ray crystallography and NMR spectroscopy. Strikingly, all active site residues of the canonical Rec-fold are pre-arranged for phosphoryl-binding and BeF ₃ ^- binding does not alter secondary or quaternary structure, indicating the absence of allosteric changes, the hallmark of RRs. Based on sequence-covariation and modeling, we analyze the intra-molecular DHp/Rec association in hybrid HKs.

---

Organizational Affiliation: 
• Structural Biology, Biozentrum, University of Basel, Spitalstr. 41, 4056, Basel, Switzerland.
Structural Biology, Biozentrum, University of Basel, Spitalstr. 41, 4056, Basel, Switzerland. [e-mail].
Structural Biology, Biozentrum, University of Basel, Spitalstr. 41, 4056, Basel, Switzerland. [e-mail].
CSSB Centre for Structural Systems Biology, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 12.96 kDa 
• Atom Count: 943 
• Modeled Residue Count: 108 
• Deposited Residue Count: 120 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histidine kinase	A	120	Caulobacter vibrioides	Mutation(s): 0  Gene Names: cckA EC: 2.7.13.3
UniProt
Find proteins for Q9X688 (Caulobacter vibrioides) Explore Q9X688  Go to UniProtKB:  Q9X688

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free:  0.188 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.43	α = 90
b = 42.9	β = 94.36
c = 65.037	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-12-16 
Deposition Author(s): Dubey, B.N., Bruederlin, M., Schirmer, T.

---

Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	31003A-166652

Revision History  

• Version 1.0: 2020-12-16
  Type: Initial release
  
• Version 2.0: 2022-10-05
  Type: Coordinate replacement
  Reason: Model completeness
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Other, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
• Version 2.1: 2024-05-01
  Changes: Data collection, Refinement description
• Version 2.2: 2025-09-10
  Changes: Database references, Structure summary