7RGS | pdb_00007rgs

The crystal structure of RocC, containing FinO domain, 24-126

• PDB DOI: https://doi.org/10.2210/pdb7RGS/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Legionella pneumophila
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-07-15 Released: 2022-11-09 
• Deposition Author(s): Kim, H.J., Edwards, R.A., Glover, J.N.M.
• Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.237 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.161 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Starting Models: experimental

Literature

Structural basis for recognition of transcriptional terminator structures by ProQ/FinO domain RNA chaperones.

Kim, H.J., Black, M., Edwards, R.A., Peillard-Fiorente, F., Panigrahi, R., Klingler, D., Eidelpes, R., Zeindl, R., Peng, S., Su, J., Omar, A.R., MacMillan, A.M., Kreutz, C., Tollinger, M., Charpentier, X., Attaiech, L., Glover, J.N.M.

(2022) Nat Commun 13: 7076-7076

• PubMed: 36400772 
• DOI: https://doi.org/10.1038/s41467-022-34875-5
• Primary Citation Related Structures: 
  7RGS, 7RGT, 7RGU


• PubMed Abstract: 
  

  The ProQ/FinO family of RNA binding proteins mediate sRNA-directed gene regulation throughout gram-negative bacteria. Here, we investigate the structural basis for RNA recognition by ProQ/FinO proteins, through the crystal structure of the ProQ/FinO domain of the Legionella pneumophila DNA uptake regulator, RocC, bound to the transcriptional terminator of its primary partner, the sRNA RocR. The structure reveals specific recognition of the 3' nucleotide of the terminator by a conserved pocket involving a β-turn-α-helix motif, while the hairpin portion of the terminator is recognized by a conserved α-helical N-cap motif. Structure-guided mutagenesis reveals key RNA contact residues that are critical for RocC/RocR to repress the uptake of environmental DNA in L. pneumophila. Structural analysis and RNA binding studies reveal that other ProQ/FinO domains also recognize related transcriptional terminators with different specificities for the length of the 3' ssRNA tail.

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Organizational Affiliation: 
• Department of Biochemistry, University of Alberta, Edmonton, AB, T6G2H7, Canada.
CIRI, Centre International de Recherche en Infectiologie, Team "Horizontal gene transfer in bacterial pathogens", Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Université de Lyon, 69100, Villeurbanne, France.
Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria.
CIRI, Centre International de Recherche en Infectiologie, Team "Horizontal gene transfer in bacterial pathogens", Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Université de Lyon, 69100, Villeurbanne, France. [e-mail].
Department of Biochemistry, University of Alberta, Edmonton, AB, T6G2H7, Canada. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration, SAXS

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 24.18 kDa 
• Atom Count: 2,087 
• Modeled Residue Count: 214 
• Deposited Residue Count: 216 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Repressor of competence, RNA Chaperone	A, B	108	Legionella pneumophila	Mutation(s): 0  Gene Names: C3926_00530, DIZ73_10055

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.237 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.161 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.559	α = 90
b = 81.772	β = 90
c = 49.419	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
HKL-2000	data scaling
HKL-2000	data processing
Coot	model building
PHASER	phasing
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-11-09 
Deposition Author(s): Kim, H.J., Edwards, R.A., Glover, J.N.M.

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Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	--

Revision History  

• Version 1.0: 2022-11-09
  Type: Initial release
  
• Version 1.1: 2022-11-30
  Changes: Database references
• Version 1.2: 2023-10-25
  Changes: Data collection, Refinement description