1U6B

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.247 

wwPDB Validation   3D Report Full Report


This is version 1.3 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:  
    1U6B

  • 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'- and the 3'-exons ...

    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: 
    • 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 --: --
    • RNA Kink Turns to the Left and to the Right
      Strobel, S.A., Adams, P.L., Stahley, M.R., Wang, J.
      () To be published --: --
    • 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
    • Self-Splicing Intron in tRNA Genes of Widely Divergent Bacteria
      Reinhold-Hurek, B., Shub, D.A.
      (1992) Nature 357: 173
    Organizational Affiliation: 

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



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
U1 small nuclear ribonucleoprotein AD [auth A]98Homo sapiensMutation(s): 2 
Gene Names: SNRPA
UniProt & NIH Common Fund Data Resources
Find proteins for P09012 (Homo sapiens)
Explore P09012 
Go to UniProtKB:  P09012
PHAROS:  P09012
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09012
Protein Feature View
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
197-MERA [auth B]197N/A
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsLengthOrganismImage
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'B [auth C]22N/A
Protein Feature View
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Entity ID: 3
MoleculeChainsLengthOrganismImage
5'-R(*CP*AP*(5MU))-3'C [auth D]3N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K
Download Ideal Coordinates CCD File 
E [auth B],
F [auth B],
G [auth B],
H [auth B],
I [auth B]		POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.247 
  • Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.541α = 90
b = 108.541β = 90
c = 249.158γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
MLPHAREphasing
REFMACrefinement
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-08-10
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Refinement description, Version format compliance
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations