4YB1 | pdb_00004yb1

20A Mutant c-di-GMP Vc2 Riboswitch bound with 3',3'-cGAMP

• PDB DOI: https://doi.org/10.2210/pdb4YB1/pdb
• NAKB: 4YB1

• Classification: RNA/RNA BINDING PROTEIN
• Organism(s): Vibrio cholerae, Homo sapiens
• Expression System: in vitro transcription vector pT7-Fluc(deltai), Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2015-02-18 Released: 2015-04-15 
• Deposition Author(s): Ren, A.M., Patel, D.J., Rajashankar, R.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 
  0.298 (Depositor), 0.311 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.235 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Literature

Structural Basis for Molecular Discrimination by a 3',3'-cGAMP Sensing Riboswitch.

Ren, A., Wang, X.C., Kellenberger, C.A., Rajashankar, K.R., Jones, R.A., Hammond, M.C., Patel, D.J.

(2015) Cell Rep 11: 1-12

• PubMed: 25818298 
• DOI: https://doi.org/10.1016/j.celrep.2015.03.004
• Primary Citation Related Structures: 
  4YAZ, 4YB0, 4YB1


• PubMed Abstract: 
  

  Cyclic dinucleotides are second messengers that target the adaptor STING and stimulate the innate immune response in mammals. Besides protein receptors, there are bacterial riboswitches that selectively recognize cyclic dinucleotides. We recently discovered a natural riboswitch that targets 3',3'-cGAMP, which is distinguished from the endogenous mammalian signal 2',3'-cGAMP by its backbone connectivity. Here, we report on structures of the aptamer domain of the 3',3'-cGAMP riboswitch from Geobacter in the 3',3'-cGAMP and c-di-GMP bound states. The riboswitch adopts a tuning fork-like architecture with a junctional ligand-binding pocket and different orientations of the arms are correlated with the identity of the bound cyclic dinucleotide. Subsequent biochemical experiments revealed that specificity of ligand recognition can be affected by point mutations outside of the binding pocket, which has implications for both the assignment and reengineering of riboswitches in this structural class.

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Organizational Affiliation: 
• Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.
Departments of Chemistry and Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
Department of Chemistry and Chemical Biology, Cornell University, NE-CAT, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA.
Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Departments of Chemistry and Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA. Electronic address: [e-mail].
Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA. Electronic address: [e-mail].

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 40.85 kDa 
• Atom Count: 2,761 
• Modeled Residue Count: 183 
• Deposited Residue Count: 183 
• 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 [auth P]	92	Homo sapiens	Mutation(s): 0  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
RNA (91-MER)	A [auth R]	91	Vibrio cholerae

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4BW	D [auth R]	2-amino-9-[(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-9-(6-amino-9H-purin-9-yl)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-2-yl]-1,9-dihydro-6H-purin-6-one C20 H24 N10 O13 P2 RFCBNSCSPXMEBK-INFSMZHSSA-N
MG	C [auth R]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free:  0.298 (Depositor), 0.311 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.235 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.738	α = 90
b = 46.836	β = 90.44
c = 80.791	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-04-15 
Deposition Author(s): Ren, A.M., Patel, D.J., Rajashankar, R.K.

Revision History  

• Version 1.0: 2015-04-15
  Type: Initial release
  
• Version 1.1: 2015-04-22
  Changes: Database references
• Version 1.2: 2015-07-22
  Changes: Non-polymer description
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary