1EFO | pdb_00001efo

CRYSTAL STRUCTURE OF AN ADENINE BULGE IN THE RNA CHAIN OF A DNA/RNA HYBRID, D(CTCCTCTTC)/R(GAAGAGAGAG)

• PDB DOI: https://doi.org/10.2210/pdb1EFO/pdb
• NAKB: 1EFO

• Classification: DNA-RNA HYBRID
• Mutation(s): No 


• Deposited: 2000-02-09 Released: 2000-05-29 
• Deposition Author(s): Sudarsanakumar, C., Xiong, Y., Sundaralingam, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.222 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Literature

Crystal structure of an adenine bulge in the RNA chain of a DNA.RNA hybrid, d(CTCCTCTTC).r(gaagagagag).

Sudarsanakumar, C., Xiong, Y., Sundaralingam, M.

(2000) J Mol Biology 299: 103-112

• PubMed: 10860725 
• DOI: https://doi.org/10.1006/jmbi.2000.3730
• Primary Citation Related Structures: 
  1EFO


• PubMed Abstract: 
  

  Crystal structure of a DNA.RNA hybrid, d(CTCCTCTTC).r(gaagagagag), with an adenine bulge in the polypurine RNA strand was determined at 2.3 A resolution. The structure was solved by the molecular replacement method and refined to a final R-factor of 19.9% (Rfree 22.2%). The hybrid duplex crystallized in the space group I222 with unit cell dimensions, a = 46.66 A, b = 47.61 A and c = 54.05 A, and adopts the A-form conformation. All RNA and DNA sugars are in the C3'-endo conformation, the glycosyl angles in anti conformation and the majority of the C4'-C5' torsion angles in g+ except two trans angles, in conformity with the C3'-endo rigid nucleotide hypothesis. The adenine bulge is looped out and it is also in the anti C3'-endo conformation. The bulge is involved in a base-triple (C.g)*a interaction with the end base-pair (C9.g10) in the minor groove of a symmetry-related molecule. The 2' hydroxyl group of g15 is hydrogen bonded to O2P and O5' of g17, skipping the bulged adenine a16 and stabilizing the sugar-phosphate backbone of the hybrid. The hydrogen bonding and the backbone conformation at the bulged adenine site is very similar to that found in the crystal structure of a protein-RNA complex.

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Organizational Affiliation: 
• Department of Chemistry, Biochemistry, Ohio State University, Columbus 43210, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 5.94 kDa 
• Atom Count: 417 
• Modeled Residue Count: 19 
• Deposited Residue Count: 19 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*TP*CP*CP*TP*CP*TP*TP*C)-3')	A	9	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*GP*AP*AP*GP*AP*GP*AP*GP*AP*G)-3')	B	10	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.222 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.66	α = 90
b = 47.61	β = 90
c = 54.04	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-05-29 
Deposition Author(s): Sudarsanakumar, C., Xiong, Y., Sundaralingam, M.

Revision History  

• Version 1.0: 2000-05-29
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2024-02-07
  Changes: Data collection, Database references