3M4W

Structural basis for the negative regulation of bacterial stress response by RseB

• PDB DOI: https://doi.org/10.2210/pdb3M4W/pdb

• Classification: Signaling Protein/Signaling Protein
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-03-12 Released: 2010-05-05 
• Deposition Author(s): Kim, D.Y., Kwon, E., Choi, J.K., Hwang, H.-Y., Kim, K.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.272 
• R-Value Work: 0.239 
• R-Value Observed: 0.239 

Starting Model: experimental

Literature

Structural basis for the negative regulation of bacterial stress response by RseB

Kim, D.Y., Kwon, E., Choi, J.K., Hwang, H.-Y., Kim, K.K.

(2010) Protein Sci 19: 1258-1263

• PubMed: 20512978 
• DOI: https://doi.org/10.1002/pro.393
• Primary Citation of Related Structures:  
  3M4W


• PubMed Abstract: 
  

  The sigmaE-dependent stress response in bacterial cells is initiated by the DegS- and RseP-regulated intramembrane proteolysis of a membrane-spanning antisigma factor, RseA. RseB binds to RseA and inhibits its sequential cleavage, thereby functioning as a negative modulator of this response. In the crystal structure of the periplasmic domain of RseA bound to RseB, the DegS cleavage site of RseA is unstructured, however, its P1 residue is buried in the hydrophobic pocket of RseB, which suggests that RseB binding blocks the access of DegS to the cleavage site.

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Organizational Affiliation: 

Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon 440-746, Korea.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B1C1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Hetero 4-mer - A2B2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 176.58 kDa 
• Atom Count: 10,535 
• Modelled Residue Count: 1,264 
• Deposited Residue Count: 1,564 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sigma-E factor regulatory protein rseB	A, B, C, D	295	Escherichia coli K-12	Mutation(s): 0  Gene Names: RseB (Amino Acids 24-318)
UniProt
Find proteins for P0AFX9 (Escherichia coli (strain K12)) Explore P0AFX9  Go to UniProtKB:  P0AFX9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Sigma-E factor negative regulatory protein	E, F, G, H	96	Escherichia coli K-12	Mutation(s): 0  Gene Names: RseA (Amino Acids 121-216)
UniProt
Find proteins for P0AFX7 (Escherichia coli (strain K12)) Explore P0AFX7  Go to UniProtKB:  P0AFX7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	I [auth A], J [auth A], K [auth B], L [auth B], M [auth E], N [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.272 
• R-Value Work: 0.239 
• R-Value Observed: 0.239 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.097	α = 90
b = 119.513	β = 90
c = 150.866	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-05-05 
Deposition Author(s): Kim, D.Y., Kwon, E., Choi, J.K., Hwang, H.-Y., Kim, K.K.

Revision History  

• Version 1.0: 2010-05-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description