205D | pdb_0000205d

STRUCTURE OF AN RNA DOUBLE HELIX INCLUDING URACIL-URACIL BASE PAIRS IN AN INTERNAL LOOP

• PDB DOI: https://doi.org/10.2210/pdb205D/pdb
• NAKB: 205D

• Classification: RNA
• Mutation(s): No 


• Deposited: 1995-04-14 Released: 1995-09-15 
• Deposition Author(s): Baeyens, K.J., De Bondt, H.L., Holbrook, S.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Work: 
  0.197 (Depositor) 
• R-Value Observed: 
  0.197 (Depositor) 

Literature

Structure of an RNA double helix including uracil-uracil base pairs in an internal loop.

Baeyens, K.J., De Bondt, H.L., Holbrook, S.R.

(1995) Nat Struct Biol 2: 56-62

• PubMed: 7719854 
• DOI: https://doi.org/10.1038/nsb0195-56
• Primary Citation Related Structures: 
  205D


• PubMed Abstract: 
  

  The crystal structure of the RNA dodecamer 5'-GGACUUUGGUCC-3' has been determined from X-ray diffraction data to 2.6 A resolution. This oligomer forms an asymmetric double helix in the crystal. Four consecutive non-Watson-Crick base-pairs are formed in the middle of the duplex including the first intrahelical U-U (or T-T) pairs observed in an oligonucleotide crystal structure. Two different conformations of U-U pairs are observed in the context of the surrounding sequence. One of these pairs is highly twisted, allowing a bound water to bridge across strands in the major groove. The crystal packing illustrates a new form of RNA helix-helix interaction.

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Organizational Affiliation: 
• Structural Biology Division, Lawrence Berkeley Laboratory, University of California, Berkeley 94720.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 7.61 kDa 
• Atom Count: 541 
• Modeled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*GP*GP*AP*CP*UP*UP*UP*GP*GP*UP*CP*C)-3')	A, B	12	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Work:  0.197 (Depositor) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.44	α = 90
b = 32.44	β = 90
c = 85.48	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1995-09-15 
Deposition Author(s): Baeyens, K.J., De Bondt, H.L., Holbrook, S.R.

Revision History  

• Version 1.0: 1995-09-15
  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: 2024-02-14
  Changes: Data collection, Database references