3P49 | pdb_00003p49

Crystal Structure of a Glycine Riboswitch from Fusobacterium nucleatum

• PDB DOI: https://doi.org/10.2210/pdb3P49/pdb
• NAKB: 3P49

• Classification: RNA BINDING PROTEIN/RNA
• Organism(s): Fusobacterium polymorphum, Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2010-10-06 Released: 2011-04-06 
• Deposition Author(s): Butler, E.B., Wang, J., Xiong, Y., Strobel, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.55 Å
• R-Value Free: 
  0.310 (Depositor), 0.352 (DCC) 
• R-Value Work: 
  0.282 (Depositor), 0.293 (DCC) 
• R-Value Observed: 
  0.284 (Depositor) 

Literature

Structural basis of cooperative ligand binding by the glycine riboswitch.

Butler, E.B., Xiong, Y., Wang, J., Strobel, S.A.

(2011) Chem Biol 18: 293-298

• PubMed: 21439473 
• DOI: https://doi.org/10.1016/j.chembiol.2011.01.013
• Primary Citation Related Structures: 
  3P49


• PubMed Abstract: 
  

  The glycine riboswitch regulates gene expression through the cooperative recognition of its amino acid ligand by a tandem pair of aptamers. A 3.6 Å crystal structure of the tandem riboswitch from the glycine permease operon of Fusobacterium nucleatum reveals the glycine binding sites and an extensive network of interactions, largely mediated by asymmetric A-minor contacts, that serve to communicate ligand binding status between the aptamers. These interactions provide a structural basis for how the glycine riboswitch cooperatively regulates gene expression.

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Organizational Affiliation: 
• Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 66.46 kDa 
• Atom Count: 4,416 
• Modeled Residue Count: 261 
• Deposited Residue Count: 267 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
U1 small nuclear ribonucleoprotein A	B	98	Homo sapiens	Mutation(s): 2  Gene Names: SNRPA
UniProt & NIH Common Fund Data Resources
Find proteins for P09012 (Homo sapiens) Explore P09012  Go to UniProtKB:  P09012
PHAROS:  P09012 GTEx:  ENSG00000077312

Entity ID: 1
Molecule	Chains	Length	Organism	Image
GLYCINE RIBOSWITCH	A	169	Fusobacterium polymorphum

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GLY	M [auth A], N [auth A]	GLYCINE C2 H5 N O2 DHMQDGOQFOQNFH-UHFFFAOYSA-N
MG	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], O [auth A], P [auth A], Q [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.55 Å
• R-Value Free:  0.310 (Depositor), 0.352 (DCC) 
• R-Value Work:  0.282 (Depositor), 0.293 (DCC) 
• R-Value Observed: 0.284 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.58	α = 90
b = 104.617	β = 90
c = 156.509	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SHELXS	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-06 
Deposition Author(s): Butler, E.B., Wang, J., Xiong, Y., Strobel, S.

Revision History  

• Version 1.0: 2011-04-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2015-06-24
  Changes: Derived calculations
• Version 1.3: 2017-06-28
  Changes: Database references, Source and taxonomy, Structure summary
• Version 1.4: 2024-02-21
  Changes: Data collection, Database references, Derived calculations