Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 102.63 kDa 
• Atom Count: 6551 
• Modelled Residue Count: 410 
• Deposited Residue Count: 416 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

3V7E

Crystal structure of YbxF bound to the SAM-I riboswitch aptamer

• PDB DOI: 10.2210/pdb3V7E/pdb
• NDB: NA1496

• Classification: RIBOSOMAL PROTEIN/RNA
• Organism(s): Bacillus subtilis, Caldanaerobacter subterraneus subsp. tengcongensis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-12-21 Released: 2012-03-07 
• Deposition Author(s): Baird, N.J., Zhang, J., Hamma, T., Ferre-D'Amare, A.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.274 
• R-Value Work: 0.218 
• R-Value Observed: 0.218 

Literature

YbxF and YlxQ are bacterial homologs of L7Ae and bind K-turns but not K-loops.

Baird, N.J., Zhang, J., Hamma, T., Ferre-D'Amare, A.R.

(2012) RNA 18: 759-770

• PubMed: 22355167 
• DOI: 10.1261/rna.031518.111
• Primary Citation of Related Structures:  
  3V7E, 3V7Q


• PubMed Abstract: 
  

The archaeal protein L7Ae and eukaryotic homologs such as L30e and 15.5kD comprise the best characterized family of K-turn-binding proteins. K-turns are an RNA motif comprised of a bulge flanked by canonical and noncanonical helices. They are widespread in cellular RNAs, including bacterial gene-regulatory RNAs such as the c-di-GMP-II, lysine, and SAM-I riboswitches, and the T-box. The existence in bacteria of K-turn-binding proteins of the L7Ae family has not been proven, although two hypothetical proteins, YbxF and YlxQ, have been proposed to be L7Ae homologs based on sequence conservation. Using purified, recombinant proteins, we show that Bacillus subtilis YbxF and YlxQ bind K-turns (K(d) ~270 nM and ~2300 nM, respectively). Crystallographic structure determination demonstrates that both YbxF and YlxQ adopt the same overall fold as L7Ae. Unlike the latter, neither bacterial protein recognizes K-loops, a structural motif that lacks the canonical helix of the K-turn. This property is shared between the bacterial and eukaryal family members. Comparison of our structure of YbxF in complex with the K-turn of the SAM-I riboswitch and previously determined structures of archaeal and eukaryal homologs bound to RNA indicates that L7Ae approaches the K-turn at a unique angle, which results in a considerably larger RNA-protein interface dominated by interactions with the noncanonical helix of the K-turn. Thus, the inability of the bacterial and eukaryal L7Ae homologs to bind K-loops probably results from their reliance on interactions with the canonical helix. The biological functions of YbxF and YlxQ remain to be determined.

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Organizational Affiliation: 

Laboratory of RNA Biophysics and Cellular Physiology, National Heart, Lung and Blood Institute, Bethesda, Maryland 20892-8012, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosome-associated protein L7Ae-like	A, B	82	Bacillus subtilis	Mutation(s): 0  Gene Names: BSU01090, rplGB, ybaB, ybxF
UniProt
Find proteins for P46350 (Bacillus subtilis (strain 168)) Explore P46350  Go to UniProtKB:  P46350

Entity ID: 2
Molecule	Chains	Length	Organism	Image
SAM-I riboswitch aptamer with an engineered helix P3	C, D	126	Caldanaerobacter subterraneus subsp. tengcongensis

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	KA [auth D], Q [auth C]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
NCO	E [auth C], EA [auth D], F [auth C], FA [auth D], G [auth C], GA [auth D], H [auth C], HA [auth D], I [auth C], IA [auth D], J [auth C], JA [auth D], K [auth C], L [auth C], M [auth C], N [auth C], O [auth C], P [auth C]	COBALT HEXAMMINE(III) Co H18 N6 DYLMFCCYOUSRTK-FGTKAUEHAT
MG	AA [auth C], BA [auth C], CA [auth C], DA [auth C], LA [auth D], MA [auth D], NA [auth D], OA [auth D], PA [auth D], QA [auth D], R [auth C], RA [auth D], S [auth C], SA [auth D], T [auth C], TA [auth D], U [auth C], V [auth C], W [auth C], X [auth C], Y [auth C], Z [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.274 
• R-Value Work: 0.218 
• R-Value Observed: 0.218 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 191.762	α = 90
b = 54.305	β = 116.56
c = 106.366	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-12-21 
• Released Date: 2012-03-07 
Deposition Author(s): Baird, N.J., Zhang, J., Hamma, T., Ferre-D'Amare, A.R.

Revision History  

• Version 1.0: 2012-03-07
  Type: Initial release
  
• Version 1.1: 2012-04-18
  Changes: Database references