3EOH

Refined group II intron structure

• PDB DOI: https://doi.org/10.2210/pdb3EOH/pdb
• NAKB: 3EOH

• Classification: RNA
• Mutation(s): No 


• Deposited: 2008-09-26 Released: 2008-10-28 
• Deposition Author(s): Toor, N., Rajashankar, K., Keating, K.S., Pyle, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.13 Å
• R-Value Free: 
  0.237 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Literature

Structural basis for exon recognition by a group II intron.

Toor, N., Rajashankar, K., Keating, K.S., Pyle, A.M.

(2008) Nat Struct Mol Biol 15: 1221-1222

• PubMed: 18953333 
• DOI: https://doi.org/10.1038/nsmb.1509
• Primary Citation of Related Structures:  
  3EOG, 3EOH


• PubMed Abstract: 
  

  Free group II introns are infectious retroelements that can bind and insert themselves into RNA and DNA molecules via reverse splicing. Here we report the 3.4-A crystal structure of a complex between an oligonucleotide target substrate and a group IIC intron, as well as the refined free intron structure. The structure of the complex reveals the conformation of motifs involved in exon recognition by group II introns.

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Organizational Affiliation: 

Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, Connecticut 06520, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 136.6 kDa 
• Atom Count: 8,301 
• Modelled Residue Count: 387 
• Deposited Residue Count: 418 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
Group IIC intron	A	412	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-R(*UP*UP*AP*UP*UP*A)-3'	B	6	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K	GA [auth A], HA [auth A], IA [auth A], JA [auth A], KA [auth A], LA [auth A], MA [auth A], NA [auth A], OA [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG	AA [auth A], BA [auth A], C [auth A], CA [auth A], D [auth A], DA [auth A], E [auth A], EA [auth A], F [auth A], FA [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], PA [auth B], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.13 Å
• R-Value Free:  0.237 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.092	α = 90
b = 94.969	β = 90
c = 225.972	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-10-28 
Deposition Author(s): Toor, N., Rajashankar, K., Keating, K.S., Pyle, A.M.

Revision History  

• Version 1.0: 2008-10-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations