248D

CRYSTAL STRUCTURES OF AN A-FORM DUPLEX WITH SINGLE-ADENOSINE BULGES AND A CONFORMATIONAL BASIS FOR SITE SPECIFIC RNA SELF-CLEAVAGE

• PDB DOI: https://doi.org/10.2210/pdb248D/pdb
• NAKB: 248D

• Classification: DNA/RNA
• Mutation(s): No 


• Deposited: 1996-02-02 Released: 1996-03-08 
• Deposition Author(s): Portmann, S., Grimm, S., Workman, C., Usman, N., Egli, M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 0.236 
• R-Value Work: 0.159 
• R-Value Observed: 0.159 

Literature

Crystal structures of an A-form duplex with single-adenosine bulges and a conformational basis for site-specific RNA self-cleavage.

Portmann, S., Grimm, S., Workman, C., Usman, N., Egli, M.

(1996) Chem Biol 3: 173-184

• PubMed: 8807843 
• DOI: https://doi.org/10.1016/s1074-5521(96)90260-4
• Primary Citation of Related Structures:  
  247D, 248D


• PubMed Abstract: 
  

  Bulged nucleotides are common secondary structural motifs in RNA molecules and are often involved in RNA-RNA and RNA-protein interactions. RNA is selectively cleaved at bulge sites (when compared to other sites within stems) in the presence of divalent metal cations. The effects of bulge nucleotides on duplex stability and topology have been extensively investigated, but no detailed X-ray structures of bulge-containing RNA fragments have been available.

---

Organizational Affiliation: 

Department of Molecular Pharmacology & Biological Chemistry, Northwestern University Medical School, 303 East Chicago Avenue, Chicago, IL 60611-3008, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 3.86 kDa 
• Atom Count: 295 
• Modelled Residue Count: 11 
• Deposited Residue Count: 11 
• Unique hybrid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA/RNA (5'-R(*GP*CP*GP*)-D(*AP*TP*AP*TP*AP*)-R(*CP*GP*C)-3'), ORTHORHOMBIC	A	11	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SPM	B [auth A], C [auth A]	SPERMINE C10 H26 N4 PFNFFQXMRSDOHW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 0.236 
• R-Value Work: 0.159 
• R-Value Observed: 0.159 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.89	α = 90
b = 33.97	β = 90
c = 57.56	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement
R-AXIS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 1996-03-08 
Deposition Author(s): Portmann, S., Grimm, S., Workman, C., Usman, N., Egli, M.

Revision History  

• Version 1.0: 1996-03-08
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2011-11-16
  Changes: Atomic model
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations