422D | pdb_0000422d

5'-R(*GP*AP*UP*CP*AP*CP*UP*UP*CP*GP*GP*U)-3'

• PDB DOI: https://doi.org/10.2210/pdb422D/pdb
• NAKB: 422D

• Classification: RNA
• Mutation(s): No 


• Deposited: 1998-09-10 Released: 2003-06-03 
• Deposition Author(s): Eswaramoorthy, S., Rao, S.T., Sundaralingam, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.188 (Depositor) 
• R-Value Work: 
  0.188 (Depositor), 0.174 (DCC) 

Starting Model: experimental

Literature

Structure of the dodecamer r(GAUCACUUCGGU) with four 5'-overhang nucleotides.

Eswaramoorthy, S., Rao, S.T., Pan, B., Sundaralingam, M.

(2004) Acta Crystallogr D Biol Crystallogr 60: 8-12

• PubMed: 14684886 
• DOI: https://doi.org/10.1107/s0907444903027860
• Primary Citation Related Structures: 
  422D


• PubMed Abstract: 
  

  The crystal structure of an RNA dodecamer, r(GAUCACUUCGGU), was solved at 2.6 A resolution by the molecular-replacement method and refined to an R(work) of 18.8% (R(free) = 22.8%) using 2494 reflections. The dodecamer crystallized in the monoclinic space group C2, with unit-cell parameters a = 71.34, b = 39.98, c = 32.47 A, beta = 104.7 degrees and two independent strands in the asymmetric unit. The dodecamer adopts an octamer duplex structure with four 5'-overhang residues (G1A2U3C4), which form Watson-Crick base pairs with another four 5'-overhang residues of a symmetry-related duplex. The octamer duplex (ACUUCGGU) contains at its center four mismatched base pairs flanked by two Watson-Crick base pairs. The mismatched bases form two G.U wobble base pairs at the ends and two U.C base pairs at the center, with one base-base hydrogen bond N4(C).O4(U) and a water bridge connecting the N(3) of the cytosine and uridine. The present study reinforces the concept of the stability of the conformation of UUCG in RNA double-helical structures.

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Organizational Affiliation: 
• Department of Chemistry and Biochemistry, The Ohio State University, 200 Johnston Laboratory, 176 West 19th Avenue, Columbus, OH 43210, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 7.58 kDa 
• Atom Count: 527 
• Modeled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.188 (Depositor) 
• R-Value Work:  0.188 (Depositor), 0.174 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.34	α = 90
b = 39.98	β = 104.7
c = 32.47	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-06-03 
Deposition Author(s): Eswaramoorthy, S., Rao, S.T., Sundaralingam, M.

Revision History  

• Version 1.0: 2003-06-03
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references
• Version 1.4: 2024-04-03
  Changes: Refinement description