1KXK | pdb_00001kxk

Crystal Structure of a RNA Molecule Containing Domain 5 and 6 of the Yeast ai5g Group II Self-splicing Intron

• PDB DOI: https://doi.org/10.2210/pdb1KXK/pdb
• NAKB: 1KXK

• Classification: RNA
• Mutation(s): No 


• Deposited: 2002-01-31 Released: 2002-03-22 
• Deposition Author(s): Zhang, L., Doudna, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.268 (Depositor) 
• R-Value Work: 
  0.248 (Depositor), 0.241 (DCC) 
• R-Value Observed: 
  0.250 (Depositor) 

Literature

Structural insights into group II intron catalysis and branch-site selection.

Zhang, L., Doudna, J.A.

(2002) Science 295: 2084-2088

• PubMed: 11859154 
• DOI: https://doi.org/10.1126/science.1069268
• Primary Citation Related Structures: 
  1KXK


• PubMed Abstract: 
  

  Group II self-splicing introns catalyze autoexcision from precursor RNA transcripts by a mechanism strikingly similar to that of the spliceosome, an RNA-protein assembly responsible for splicing together the protein-coding parts of most eukaryotic pre-mRNAs. Splicing in both cases initiates via nucleophilic attack at the 5' splice site by the 2' OH of a conserved intron adenosine residue, creating a branched (lariat) intermediate. Here, we describe the crystal structure at 3.0 A resolution of a 70-nucleotide RNA containing the catalytically essential domains 5 and 6 of the yeast ai5gamma group II self-splicing intron, revealing an unexpected two-nucleotide bulged structure around the branch-point adenosine in domain 6.

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Organizational Affiliation: 
• Department of Molecular Biophysics and Biochemistry and, Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 22.67 kDa 
• Atom Count: 1,499 
• Modeled Residue Count: 70 
• Deposited Residue Count: 70 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
ai5g group II Self-splicing intron	A	70	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	B [auth A], C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.268 (Depositor) 
• R-Value Work:  0.248 (Depositor), 0.241 (DCC) 
• R-Value Observed: 0.250 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.987	α = 90
b = 90.987	β = 90
c = 235.891	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-03-22 
Deposition Author(s): Zhang, L., Doudna, J.A.

Revision History  

• Version 1.0: 2002-03-22
  Type: Initial release
  
• Version 1.1: 2008-04-27
  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