1P79 | pdb_00001p79

Crystal structure of a bulged RNA tetraplex: implications for a novel binding site in RNA tetraplex

• PDB DOI: https://doi.org/10.2210/pdb1P79/pdb
• NAKB: 1P79

• Classification: RNA
• Mutation(s): No 


• Deposited: 2003-04-30 Released: 2003-11-04 
• Deposition Author(s): Pan, B., Xiong, Y., Shi, K., Sundaralingam, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 
  0.136 (Depositor), 0.335 (DCC) 
• R-Value Work: 
  0.127 (Depositor), 0.315 (DCC) 
• R-Value Observed: 
  0.127 (Depositor) 

Literature

Crystal Structure of a Bulged RNA Tetraplex at 1.1 A Resolution: Implications for a Novel Binding Site in RNA Tetraplex

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

(2003) Structure 11: 1423-1430

• PubMed: 14604532 
• DOI: https://doi.org/10.1016/j.str.2003.09.017
• Primary Citation Related Structures: 
  1P79


• PubMed Abstract: 
  

  Bulges are an important structural motif in RNA and can be used as recognition and interaction sites in RNA-protein interaction and RNA-RNA interaction. Here we report the first crystal structure of a bulged RNA tetraplex at 1.1 A resolution. The hexamer r(U)(BrdG)r(UGGU) forms a parallel tetraplex with the uridine sandwiched by guanines bulging out. The bulged uridine adopts the syn glycosidic conformation and its O2 and N3 atoms face outwards, serving as an effective recognition and interaction site. The bulge formation both widens the groove width and changes the groove hydrogen-bonding pattern on its 5' side. However, the bulge does not make any bends or kinks in the tetraplex structure. The present study demonstrates the dramatic difference between uridine and guanine in forming tetraplex structure. In addition, both G(syn) tetrad and G(anti) tetrad have been observed. They display the same base-pairing pattern and similar C1'-C1' distance but different hydrogen-bonding patterns in the groove.

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

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 2.03 kDa 
• Atom Count: 141 
• Modeled Residue Count: 5 
• Deposited Residue Count: 6 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-R(*UP*GP*UP*GP*GP*U)-3'	A	6	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K	B [auth A], C [auth A], D [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free:  0.136 (Depositor), 0.335 (DCC) 
• R-Value Work:  0.127 (Depositor), 0.315 (DCC) 
• R-Value Observed: 0.127 (Depositor) 

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.014	α = 90
b = 35.014	β = 90
c = 22.257	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-11-04 
Deposition Author(s): Pan, B., Xiong, Y., Shi, K., Sundaralingam, M.

Revision History  

• Version 1.0: 2003-11-04
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations