283D | pdb_0000283d

A CURVED RNA HELIX INCORPORATING AN INTERNAL LOOP WITH G-A AND A-A NON-WATSON-CRICK BASE PAIRING

• PDB DOI: https://doi.org/10.2210/pdb283D/pdb
• NAKB: 283D

• Classification: RNA
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 1996-09-03 Released: 1996-09-30 
• Deposition Author(s): Baeyens, K.J., De Bondt, H.L., Pardi, A., Holbrook, S.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.198 (Depositor) 
• R-Value Work: 
  0.186 (Depositor) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

A curved RNA helix incorporating an internal loop with G.A and A.A non-Watson-Crick base pairing.

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

(1996) Proc Natl Acad Sci U S A 93: 12851-12855

• PubMed: 8917508 
• DOI: https://doi.org/10.1073/pnas.93.23.12851
• Primary Citation Related Structures: 
  283D


• PubMed Abstract: 
  

  The crystal structure of the RNA dodecamer 5'-GGCC(GAAA)GGCC-3' has been determined from x-ray diffraction data to 2.3-A resolution. In the crystal, these oligomers form double helices around twofold symmetry axes. Four consecutive non-Watson-Crick base pairs make up an internal loop in the middle of the duplex, including sheared G.A pairs and novel asymmetric A.A pairs. This internal loop sequence produces a significant curvature and narrowing of the double helix. The helix is curved by 34 degrees from end to end and the diameter is narrowed by 24% in the internal loop. A Mn2+ ion is bound directly to the N7 of the first guanine in the Watson-Crick region following the internal loop and the phosphate of the preceding residue. This Mn2+ location corresponds to a metal binding site observed in the hammerhead catalytic RNA.

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

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 3.94 kDa 
• Atom Count: 277 
• Modeled Residue Count: 12 
• Deposited Residue Count: 12 
• Unique nucleic acid chains: 1

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	B [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.198 (Depositor) 
• R-Value Work:  0.186 (Depositor) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.71	α = 90
b = 37.71	β = 90
c = 88.3	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	refinement
R-AXIS	data reduction
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1996-09-30 
Deposition Author(s): Baeyens, K.J., De Bondt, H.L., Pardi, A., Holbrook, S.R.

Revision History  

• Version 1.0: 1996-09-30
  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, Derived calculations
• Version 1.4: 2024-04-03
  Changes: Refinement description