5I4C | pdb_00005i4c

Crystal structure of non-phosphorylated receiver domain of the stress response regulator RcsB from Escherichia coli

• PDB DOI: https://doi.org/10.2210/pdb5I4C/pdb

• Classification: GENE REGULATION
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-02-11 Released: 2016-10-12 
• Deposition Author(s): Filippova, E.V., Wawrzak, Z., Minasov, G., Ruan, J., Pshenychnyi, S., Wolfe, A.J., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.238 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Literature

Crystal structure of nonphosphorylated receiver domain of the stress response regulator RcsB from Escherichia coli.

Filippova, E.V., Wawrzak, Z., Ruan, J., Pshenychnyi, S., Schultz, R.M., Wolfe, A.J., Anderson, W.F.

(2016) Protein Sci 25: 2216-2224

• PubMed: 27670836 
• DOI: https://doi.org/10.1002/pro.3050
• Primary Citation Related Structures: 
  5I4C


• PubMed Abstract: 
  

  RcsB, the transcription-associated response regulator of the Rcs phosphorelay two-component signal transduction system, activates cell stress responses associated with desiccation, cell wall biosynthesis, cell division, virulence, biofilm formation, and antibiotic resistance in enteric bacterial pathogens. RcsB belongs to the FixJ/NarL family of transcriptional regulators, which are characterized by a highly conserved C-terminal DNA-binding domain. The N-terminal domain of RcsB belongs to the family of two-component receiver domains. This receiver domain contains the phosphoacceptor site and participates in RcsB dimer formation; it also contributes to dimer formation with other transcription factor partners. Here, we describe the crystal structure of the Escherichia coli RcsB receiver domain in its nonphosphorylated state. The structure reveals important molecular details of phosphorylation-independent dimerization of RcsB and has implication for the formation of heterodimers.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Genetics, Center for Structural Genomics of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, 60611.
Life Science Collaborative Access Team, Synchrotron Research Center, Northwestern University, Argonne, Illinois, 60439.
Yale University School of Medicine, Department of Digestive Diseases, New Haven, CT 06510.
Recombinant Protein Production Core, Northwestern University, Chemistry of Life Processes Institute, Evanston, Illinois 60208.
Department of Microbiology and Immunology, Loyola University Chicago, Health Sciences Division, Stritch School of Medicine, Maywood, Illinois, 60153.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration, light scattering

Macromolecule Content 

• Total Structure Weight: 16.04 kDa 
• Atom Count: 1,101 
• Modeled Residue Count: 131 
• Deposited Residue Count: 147 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulatory protein RcsB	A	147	Escherichia coli K-12	Mutation(s): 0  Gene Names: rcsB, b2217, JW2205
UniProt
Find proteins for P0DMC7 (Escherichia coli (strain K12)) Explore P0DMC7  Go to UniProtKB:  P0DMC7

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.238 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m35i4c

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.197	α = 90
b = 61.197	β = 90
c = 65.226	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PHENIX	model building
BALBES	phasing
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-10-12 
Deposition Author(s): Filippova, E.V., Wawrzak, Z., Minasov, G., Ruan, J., Pshenychnyi, S., Wolfe, A.J., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2016-10-12
  Type: Initial release
  
• Version 1.1: 2016-11-30
  Changes: Database references
• Version 1.2: 2017-11-01
  Changes: Author supporting evidence, Database references
• Version 1.3: 2024-03-06
  Changes: Data collection, Database references