7TH0 | pdb_00007th0

Escherichia coli RpnA-S

• PDB DOI: https://doi.org/10.2210/pdb7TH0/pdb

• Classification: ANTITOXIN
• Organism(s): Escherichia coli str. K-12 substr. MG1655
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-01-10 Released: 2023-03-29 
• Deposition Author(s): Zhong, A., Hickman, A.B., Storz, G., Dyda, F.
• Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.247 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.228 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Starting Model: other

Literature

Toxic antiphage defense proteins inhibited by intragenic antitoxin proteins.

Zhong, A., Jiang, X., Hickman, A.B., Klier, K., Teodoro, G.I.C., Dyda, F., Laub, M.T., Storz, G.

(2023) Proc Natl Acad Sci U S A 120: e2307382120-e2307382120

• PubMed: 37487082 
• DOI: https://doi.org/10.1073/pnas.2307382120
• Primary Citation Related Structures: 
  7TH0


• PubMed Abstract: 
  

  Recombination-promoting nuclease (Rpn) proteins are broadly distributed across bacterial phyla, yet their functions remain unclear. Here, we report that these proteins are toxin-antitoxin systems, comprised of genes-within-genes, that combat phage infection. We show the small, highly variable Rpn C -terminal domains (Rpn _S ), which are translated separately from the full-length proteins (Rpn _L ), directly block the activities of the toxic Rpn _L . The crystal structure of RpnA _S revealed a dimerization interface encompassing α helix that can have four amino acid repeats whose number varies widely among strains of the same species. Consistent with strong selection for the variation, we document that plasmid-encoded RpnP2 _L protects Escherichia coli against certain phages. We propose that many more intragenic-encoded proteins that serve regulatory roles remain to be discovered in all organisms.

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Organizational Affiliation: 
• Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892.
Intramural Research Program, National Library of Medicine, NIH, Bethesda, MD 20894.
Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892.
Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139.
HHMI, Massachusetts Institute of Technology, Cambridge, MA 02139.

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: light scattering

Macromolecule Content 

• Total Structure Weight: 5.52 kDa 
• Atom Count: 361 
• Modeled Residue Count: 46 
• Deposited Residue Count: 49 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Recombination-promoting nuclease RpnA	A	49	Escherichia coli str. K-12 substr. MG1655	Mutation(s): 0  Gene Names: rpnA, yhgA, b3411, JW3374 EC: 3.1.21
UniProt
Find proteins for P31667 (Escherichia coli (strain K12)) Explore P31667  Go to UniProtKB:  P31667

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.247 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.228 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.02	α = 90
b = 58.27	β = 90
c = 38.71	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-03-29 
Deposition Author(s): Zhong, A., Hickman, A.B., Storz, G., Dyda, F.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	--
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)	United States	--

Revision History  

• Version 1.0: 2023-03-29
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Database references
• Version 1.2: 2023-11-15
  Changes: Data collection
• Version 1.3: 2024-11-13
  Changes: Structure summary