Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 144.13 kDa 
• Atom Count: 9583 
• Residue Count: 1241 
• Unique protein chains: 1

5O8Y

Conformational dynamism for DNA interaction in Salmonella typhimurium RcsB response regulator.

• DOI: 10.2210/pdb5O8Y/pdb

• Classification: TRANSCRIPTION
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-06-14 Released: 2017-11-15 
• Deposition Author(s): Casino, P., Marina, A., Miguel-Romero, L., Huesa, J.
• Funding Organization(s): Ministry of Economy and Competitiveness

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.253 
• R-Value Work: 0.223 
• R-Value Observed: 0.225 

Literature

Conformational dynamism for DNA interaction in the Salmonella RcsB response regulator.

Casino, P., Miguel-Romero, L., Huesa, J., Garcia, P., Garcia-Del Portillo, F., Marina, A.

(2018) Nucleic Acids Res 46: 456-472

• PubMed: 29186528 
• DOI: 10.1093/nar/gkx1164
• Primary Citation of Related Structures:  
  6EO3, 6EO2, 5O8Y, 5O8Z


• PubMed Abstract: 
  

The RcsCDB phosphorelay system controls an extremely large regulon in Enterobacteriaceae that involves processes such as biofilm formation, flagella production, synthesis of extracellular capsules and cell division. Therefore, fine-tuning of this system is essential for virulence in pathogenic microorganisms of this group. The final master effector of the RcsCDB system is the response regulator (RR) RcsB, which activates or represses multiple genes by binding to different promoter regions. This regulatory activity of RcsB can be done alone or in combination with additional transcriptional factors in phosphorylated or dephosphorylated states. The capacity of RcsB to interact with multiple promoters and partners, either dephosphorylated or phosphorylated, suggests an extremely conformational dynamism for this RR. To shed light on the activation mechanism of RcsB and its implication on promoter recognition, we solved the crystal structure of full-length RcsB from Salmonella enterica serovar Typhimurium in the presence and absence of a phosphomimetic molecule BeF3-. These two novel structures have guided an extensive site-directed mutagenesis study at the structural and functional level that confirms RcsB conformational plasticity and dynamism. Our data allowed us to propose a β5-T switch mechanism where phosphorylation is coupled to alternative DNA binding ways and which highlights the conformational dynamism of RcsB to be so pleiotropic.

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Organizational Affiliation: 

Group 739 of the Centro de Investigación Biomédica en Red sobre Enfermedades Raras (CIBERER) del Instituto de Salud Carlos III, Spain.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulatory protein RcsB	A, C, D, F, G, H	216	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0  Gene Names: rcsB, STM2270
Find proteins for P58663 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P58663  Go to UniProtKB:  P58663

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PE4	A, C	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL C16 H34 O8 PJWQOENWHPEPKI-UHFFFAOYSA-N
SO4	A, C, D, F, G, H	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.253 
• R-Value Work: 0.223 
• R-Value Observed: 0.225 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.83	α = 90
b = 108.83	β = 90
c = 306.538	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-06-14 
• Released Date: 2017-11-15 
Deposition Author(s): Casino, P., Marina, A., Miguel-Romero, L., Huesa, J.

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Funding Organization	Location	Grant Number
Ministry of Economy and Competitiveness	Spain	BFU2016-78606-P
Ministry of Economy and Competitiveness	Spain	BIO2016-78571-P
Ministry of Economy and Competitiveness	Spain	BIO2013-42619-P

Revision History 

• Version 1.0: 2017-11-15
  Type: Initial release
  
• Version 1.1: 2017-12-13
  Changes: Database references
• Version 1.2: 2018-01-24
  Changes: Database references