165D | pdb_0000165d

THE STRUCTURE OF A MISPAIRED RNA DOUBLE HELIX AT 1.6 ANGSTROMS RESOLUTION AND IMPLICATIONS FOR THE PREDICTION OF RNA SECONDARY STRUCTURE

• PDB DOI: https://doi.org/10.2210/pdb165D/pdb
• NAKB: 165D

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


• Deposited: 1994-03-21 Released: 1994-08-31 
• Deposition Author(s): Cruse, W., Saludjian, P., Biala, E., Strazewski, P., Prange, T., Kennard, O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Work: 
  0.180 (Depositor) 
• R-Value Observed: 
  0.180 (Depositor) 

Literature

Structure of a mispaired RNA double helix at 1.6-A resolution and implications for the prediction of RNA secondary structure.

Cruse, W.B., Saludjian, P., Biala, E., Strazewski, P., Prange, T., Kennard, O.

(1994) Proc Natl Acad Sci U S A 91: 4160-4164

• PubMed: 7514296 
• DOI: https://doi.org/10.1073/pnas.91.10.4160
• Primary Citation Related Structures: 
  165D


• PubMed Abstract: 
  

  The nonamer r(GCUUCGGC)dBrU, where dBrU is 5-bromo-2'-deoxyuridine, contains the tetraloop sequence UUCG. It crystallizes in the presence of Rh(NH3)6Cl3. In solution the oligomer is expected to form a hairpin loop but the x-ray structure analysis, to a resolution of 1.6 A, indicates an eight-base-pair A-RNA duplex containing a central block of two G.U and two C.U pairs. Self-pairs which approximate to Watson-Crick geometry are also formed in the extended crystal structure between symmetry-related BrU residues and are part of infinite double-helical stacks. The G.U pair is a wobble base pair analogous to the G.T pair found in DNA fragments. The C.U mismatch involves one hydrogen-bonded contact between the bases and a bridging water molecule which ensures a good fit of the base pair in the RNA helix. The BrU.BrU pair is held by two hydrogen bonds in an orientation which is compatible with duplex geometry. The structure observed within the crystal has some parallels with the structure of globular RNAs, and the presence of stable, noncanonical base pairs has implications for the prediction of RNA secondary structure.

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Organizational Affiliation: 
• Cambridge Crystallographic Data Centre, United Kingdom.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 6.6 kDa 
• Atom Count: 474 
• Modeled Residue Count: 18 
• Deposited Residue Count: 18 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA/RNA (5'-R(*GP*CP*UP*UP*CP*GP*GP*CP*)-D(*(BRU))-3')	A, B	9	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RHD	C [auth A], D [auth A], E [auth A], F [auth B]	RHODIUM HEXAMINE ION H18 N6 Rh JGYYKTIOJIEIKU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Work:  0.180 (Depositor) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.8	α = 90
b = 19.4	β = 109.9
c = 50.14	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1994-08-31 
Deposition Author(s): Cruse, W., Saludjian, P., Biala, E., Strazewski, P., Prange, T., Kennard, O.

Revision History  

• Version 1.0: 1994-08-31
  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: 2018-04-18
  Changes: Data collection
• Version 1.4: 2024-02-07
  Changes: Data collection, Database references, Derived calculations