1U6B

CRYSTAL STRUCTURE OF A SELF-SPLICING GROUP I INTRON WITH BOTH EXONS

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.246 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Crystal Structure of a Self-Splicing Group I Intron with Both Exons.

Adams, P.L., Stahley, M.R., Kosek, A.B., Wang, J., Strobel, S.A.

(2004) Nature 430: 45-50

  • DOI: 10.1038/nature02642
  • Primary Citation of Related Structures:  
  • Also Cited By: 1ZZN

  • PubMed Abstract: 

    • The discovery of the RNA self-splicing group I intron provided the first demonstration that not all enzymes are proteins. Here we report the X-ray crystal structure (3.1-A resolution) of a complete group I bacterial intron in complex with both the 5' ...

    The discovery of the RNA self-splicing group I intron provided the first demonstration that not all enzymes are proteins. Here we report the X-ray crystal structure (3.1-A resolution) of a complete group I bacterial intron in complex with both the 5'- and the 3'-exons. This complex corresponds to the splicing intermediate before the exon ligation step. It reveals how the intron uses structurally unprecedented RNA motifs to select the 5'- and 3'-splice sites. The 5'-exon's 3'-OH is positioned for inline nucleophilic attack on the conformationally constrained scissile phosphate at the intron-3'-exon junction. Six phosphates from three disparate RNA strands converge to coordinate two metal ions that are asymmetrically positioned on opposing sides of the reactive phosphate. This structure represents the first splicing complex to include a complete intron, both exons and an organized active site occupied with metal ions.

    Related Citations: 
    • RNA Kink Turns to the Left and to the Right
      Strobel, S.A.,Adams, P.L.,Stahley, M.R.,Wang, J.
      () TO BE PUBLISHED --: --
    • Crystal Structure of a Group I Intron Splicing Intermediate
      Adams, P.L.,Stahely, M.R.,Gill, M.L.,Berman, C.,Kosek, A.B.,Wang, J.,Strobel, S.A.
      () TO BE PUBLISHED --: --
    • Self-Splicing Intron in tRNA Genes of Widely Divergent Bacteria
      Reinhold-Hurek, B.,Shub, D.A.
      (1992) Nature 357: 173
    • In Vitro Splicing of the Ribosomal RNA Precursor of Tetrahymena: Involvement of a Guanosine Nucleotide in the Excision of Intervening Sequence
      Cech, T.R.,Zaug, A.J.,Grabowaski, P.J.
      (1981) Cell 27: 487

    Organizational Affiliation: 

    Department of Molecular Biophysics and Biochemistry, 260 Whitney Avenue, Yale University, New Haven, Connecticut 06520-8114, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
U1 small nuclear ribonucleoprotein A
A
98Homo sapiensMutation(s): 2 
Gene Names: SNRPA
Find proteins for P09012 (Homo sapiens)
Go to Gene View: SNRPA
Go to UniProtKB:  P09012
Entity ID: 1
MoleculeChainsLengthOrganism
197-MERB197N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-R(*AP*AP*GP*CP*CP*AP*CP*AP*CP*AP*AP*AP*CP*CP*AP*GP*AP*CP*GP *GP*CP*C)-3'C22N/A
Entity ID: 3
MoleculeChainsLengthOrganism
5'-R(*CP*AP*(5MU))-3'D3N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K
Download SDF File 
Download CCD File 
B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG
Download SDF File 
Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
A23
Query on A23
B
RNA LINKINGC10 H13 N5 O9 P2A
GTP
Query on GTP
B
NON-POLYMERC10 H16 N5 O14 P3G
5MU
Query on 5MU
D
RNA LINKINGC10 H15 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.246 
  • Space Group: P 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 108.541α = 90.00
b = 108.541β = 90.00
c = 249.158γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MLPHAREphasing
HKL-2000data collection

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-08-10
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Refinement description, Version format compliance