413D | pdb_0000413d

A'-FORM RNA DOUBLE HELIX IN THE SINGLE CRYSTAL STRUCTURE OF R(UGAGCUUCGGCUC)

• PDB DOI: https://doi.org/10.2210/pdb413D/pdb
• Entry: 413D supersedes: 373D
• NAKB: 413D

• Classification: RNA
• Mutation(s): No 


• Deposited: 1998-07-10 Released: 1998-07-10 
• Deposition Author(s): Tanaka, Y., Fujii, S., Hiroaki, H., Sakata, T., Tanaka, T., Uesugi, S., Tomita, K.-I., Kyogoku, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.224 (Depositor) 
• R-Value Work: 
  0.182 (Depositor) 
• R-Value Observed: 
  0.182 (Depositor) 

Literature

A'-form RNA double helix in the single crystal structure of r(UGAGCUUCGGCUC).

Tanaka, Y., Fujii, S., Hiroaki, H., Sakata, T., Tanaka, T., Uesugi, S., Tomita, K., Kyogoku, Y.

(1999) Nucleic Acids Res 27: 949-955

• PubMed: 9927725 
• DOI: https://doi.org/10.1093/nar/27.4.949
• Primary Citation Related Structures: 
  413D


• PubMed Abstract: 
  

  Here we demonstrate the presence of the A'-RNA conformation using the single crystal structure of a tridecamer: r(UGAGCUUCGGCUC). The average A'-RNA conformation deduced from X-ray fiber diffraction data had only been available previously, but now the presence of the A'-RNA conformation has been found in a single crystal structure for the first time. Statistical analysis showed that the A'-RNA conformation is distinguishable from the A-RNA conformation in a plot of the major groove width against the base pair inclination angle. The major groove of the A'-RNA conformation is wide enough to accommodate a protein or peptide while that of the A-RNA conformation is too narrow to do so. The presence of the A'-RNA conformation is significant for protein-RNA interaction.

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Organizational Affiliation: 
• Division of Molecular Biophysics, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565, Japan. [e-mail]

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 4.11 kDa 
• Atom Count: 325 
• Modeled Residue Count: 13 
• Deposited Residue Count: 13 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*UP*GP*AP*GP*CP*UP*UP*CP*GP*GP*CP*UP*C)-3')	A	13	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.224 (Depositor) 
• R-Value Work:  0.182 (Depositor) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.49	α = 90
b = 32.3	β = 117.56
c = 38.76	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
RIGAKU	data reduction
RIGAKU	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-07-10 
Deposition Author(s): Tanaka, Y., Fujii, S., Hiroaki, H., Sakata, T., Tanaka, T., Uesugi, S., Tomita, K.-I., Kyogoku, Y.
• This entry supersedes: 373D

Revision History  

• Version 1.0: 1998-07-10
  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: 2024-02-28
  Changes: Data collection, Database references