8VFS | pdb_00008vfs

oppF ROSE-like RNA thermometer structure

• PDB DOI: https://doi.org/10.2210/pdb8VFS/pdb
• NAKB: 8VFS

• Classification: RNA
• Organism(s): Providencia stuartii
• Mutation(s): No 


• Deposited: 2023-12-21 Released: 2024-12-25 
• Deposition Author(s): Shaffer, S.N., Passalacqua, L.F.M., Abdelsayed, M.M., Ferre-D'Amare, A.R.
• Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

Literature

RNA thermometers are widespread upstream of ABC transporter genes in bacteria.

Tong, A.Y., Tong, E.L., Hannani, M.A., Shaffer, S.N., Santiago, D., Ferre-D'Amare, A.R., Passalacqua, L.F.M., Abdelsayed, M.M.

(2024) J Biological Chem 300: 107547-107547

• PubMed: 38992441 
• DOI: https://doi.org/10.1016/j.jbc.2024.107547
• Primary Citation of Related Structures:  
  8VFS


• PubMed Abstract: 
  

  RNA thermometers are temperature-sensing non-coding RNAs that regulate the expression of downstream genes. A well-characterized RNA thermometer motif discovered in bacteria is the ROSE-like element (repression of heat shock gene expression). ATP-binding cassette (ABC) transporters are a superfamily of transmembrane proteins that harness ATP hydrolysis to facilitate the export and import of substrates across cellular membranes. Through structure-guided bioinformatics, we discovered that ROSE-like RNA thermometers are widespread upstream of ABC transporter genes in bacteria. X-ray crystallography, biochemistry, and cellular assays indicate that these RNA thermometers are functional regulatory elements. This study expands the known biological role of RNA thermometers to these key membrane transporters.

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Organizational Affiliation: 
• Department of Biology, California Lutheran University, Thousand Oaks, California, USA.
Laboratory of Nucleic Acids, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA.
Laboratory of Nucleic Acids, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA. Electronic address: [e-mail].
Department of Biology, California Lutheran University, Thousand Oaks, California, USA. Electronic address: [e-mail].

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 17.36 kDa 
• Atom Count: 1,141 
• Modeled Residue Count: 54 
• Deposited Residue Count: 54 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (27-MER)	A, B	27	Providencia stuartii

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.602	α = 90
b = 63.602	β = 90
c = 86.147	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
DIALS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-25 
Deposition Author(s): Shaffer, S.N., Passalacqua, L.F.M., Abdelsayed, M.M., Ferre-D'Amare, A.R.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	--

Revision History  

• Version 1.0: 2024-12-25
  Type: Initial release
  
• Version 1.1: 2025-01-22
  Changes: Database references