1J6S | pdb_00001j6s

Crystal Structure of an RNA Tetraplex (UGAGGU)4 with A-tetrads, G-tetrads, U-tetrads and G-U octads

• PDB DOI: https://doi.org/10.2210/pdb1J6S/pdb
• NAKB: 1J6S

• Classification: RNA
• Mutation(s): No 


• Deposited: 2002-07-10 Released: 2003-08-05 
• Deposition Author(s): Pan, B., Xiong, Y., Shi, K., Deng, J., Sundaralingam, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.184 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.166 (Depositor) 

Literature

Crystal structure of an RNA purine-rich tetraplex containing adenine tetrads: implications for specific binding in RNA tetraplexes

Pan, B., Xiong, Y., Shi, K., Deng, J., Sundaralingam, M.

(2003) Structure 11: 815-823

• PubMed: 12842044 
• DOI: https://doi.org/10.1016/s0969-2126(03)00107-2
• Primary Citation Related Structures: 
  1J6S


• PubMed Abstract: 
  

  Purine-rich regions in DNA and RNA may contain both guanines and adenines, which have various biological functions. Here we report the crystal structure of an RNA purine-rich fragment containing both guanine and adenine at 1.4 A resolution. Adenines form an adenine tetrad in the N6-H em leader N7 conformation. Substitution of an adenine tetrad in the guanine tetraplex does not change the global conformation but introduces irregularity in both the hydrogen bonding interaction pattern in the groove and the metal ion binding pattern in the central cavity of the tetraplex. The irregularity in groove binding may be critical for specific binding in tetraplexes. The formation of G-U octads provides a mechanism for interaction in the groove. Ba(2+) ions prefer to bind guanine tetrads, and adenine tetrads can only be bound by Na(+) ions, illustrating the binding selectivity of metal ions for the tetraplex.

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Organizational Affiliation: 
• Departments of Chemistry and Biochemistry, The Ohio State University, 200 Johnston Lab, 176 West 19th Avenue, Columbus, OH 43210, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 9.26 kDa 
• Atom Count: 625 
• Modeled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-R(*(BRUP*GP*AP*GP*GP*U)-3'	A, B, C, D	6	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BA	E [auth A], F [auth A], I [auth B], J [auth B], M [auth C], N [auth C], R [auth D], S [auth D]	BARIUM ION Ba XDFCIPNJCBUZJN-UHFFFAOYSA-N
NA	G [auth A], H [auth A], K [auth B], L [auth B], O [auth C], P [auth C], Q [auth C], T [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.184 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.166 (Depositor) 

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.984	α = 90
b = 37.984	β = 90
c = 82.195	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SOLVE	phasing
RESOLVE	model building
CNS	refinement
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-08-05 
Deposition Author(s): Pan, B., Xiong, Y., Shi, K., Deng, J., Sundaralingam, M.

Revision History  

• Version 1.0: 2003-08-05
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations