Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 36.96 kDa 
• Atom Count: 2389 
• Modelled Residue Count: 273 
• Deposited Residue Count: 336 
• Unique protein chains: 1

4ZHV

Crystal structure of a bacterial signalling protein

• DOI: 10.2210/pdb4ZHV/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-04-27 Released: 2016-04-27 
• Deposition Author(s): Li, S., Li, T., Wang, Y., Bartlam, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 0.188 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 

Literature

Structural insights into YfiR sequestering by YfiB in Pseudomonas aeruginosa PAO1

Li, S., Li, T., Xu, Y., Zhang, Q., Zhang, W., Che, S., Liu, R., Wang, Y., Bartlam, M.

(2015) Sci Rep 5: 16915-16915

• PubMed: 26593397 
• DOI: 10.1038/srep16915
• Primary Citation of Related Structures:  
  4ZHU, 4ZHV, 4ZHW, 4ZHY


• PubMed Abstract: 
  

YfiBNR is a tripartite signalling system in Pseudomonas aeruginosa that modulates intracellular c-di-GMP levels in response to signals received in the periplasm. YfiB is an outer membrane lipoprotein and presumed sensor protein that sequesters the repressor protein YfiR. To provide insights into YfiBNR function, we have determined three-dimensional crystal structures of YfiB and YfiR from P. aeruginosa PAO1 alone and as a 1:1 complex. A YfiB(27-168) construct is predominantly dimeric, whereas a YfiB(59-168) is monomeric, indicating that YfiB can dimerize via its N-terminal region. YfiR forms a stable complex with YfiB(59-168), while the YfiR binding interface is obstructed by the N-terminal region in YfiB(27-168). The YfiB-YfiR complex reveals a conserved interaction surface on YfiR that overlaps with residues predicted to interact with the periplasmic PAS domain of YfiN. Comparison of native and YfiR-bound structures of YfiB suggests unwinding of the N-terminal linker region for attachment to the outer membrane. A model is thus proposed for YfiR sequestration at the outer membrane by YfiB. Our work provides the first detailed insights into the interaction between YfiB and YfiR at the molecular level and is a valuable starting point for further functional and mechanistic studies of the YfiBNR signalling system.

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Organizational Affiliation: 

College of Life Sciences, Nankai University, Tianjin, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YfiB	A, B	168	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: yfiB, PA1119
UniProt
Find proteins for Q9I4L6 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I4L6  Go to UniProtKB:  Q9I4L6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 0.188 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.841	α = 90
b = 56.418	β = 90
c = 139.568	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-04-27 
• Released Date: 2016-04-27 
Deposition Author(s): Li, S., Li, T., Wang, Y., Bartlam, M.

Revision History  

• Version 1.0: 2016-04-27
  Type: Initial release