2GJW

RNA Recognition and Cleavage by an Splicing Endonuclease

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.250 

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This is version 1.3 of the entry. See complete history. 


Literature

RNA Recognition and Cleavage by an Splicing Endonuclease

Xue, S., Calvin, K., Li, H.

(2006) Science 312: 902-910

  • DOI: https://doi.org/10.1126/science.1126629
  • Primary Citation of Related Structures:  
    2GJW

  • PubMed Abstract: 

    The RNA splicing endonuclease cleaves two phosphodiester bonds within folded precursor RNAs during intron removal, producing the functional RNAs required for protein synthesis. Here we describe at a resolution of 2.85 angstroms the structure of a splicing endonuclease from Archaeglobus fulgidus bound with a bulge-helix-bulge RNA containing a noncleaved and a cleaved splice site. The endonuclease dimer cooperatively recognized a flipped-out bulge base and stabilizes sharply bent bulge backbones that are poised for an in-line RNA cleavage reaction. Cooperativity arises because an arginine pair from one catalytic domain sandwiches a nucleobase within the bulge cleaved by the other catalytic domain.

    • Organizational Affiliation: 

    Department of Chemistry and Biochemistry, Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA.


Macromolecules

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA-splicing endonucleaseG [auth A],
H [auth B],
I [auth C],
J [auth D]		313Archaeoglobus fulgidusMutation(s): 0 
Gene Names: endA
EC: 3.1.27.9
UniProt
Find proteins for O29362 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16))
Explore O29362 
Go to UniProtKB:  O29362
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO29362
Sequence Annotations
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  • Reference Sequence

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Entity ID: 1
MoleculeChains LengthOrganismImage
5'-R(*GP*CP*GP*AP*CP*CP*GP*AP*CP*CP*AP*(DU)P*AP*GP*CP*UP*GP*CP*A)-3'A [auth E],
D [auth I]		19N/A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
5'-R(*UP*GP*CP*AP*GP*CP*GP*GP*UP*CP*AP*(A23))-3'B [auth F],
E [auth J]		12N/A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
5'-R(*AP*GP*GP*UP*CP*GP*C)-3'C [auth H],
F [auth L]		7N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.250 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.965α = 90
b = 140.413β = 111.68
c = 82.048γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
ADSCdata collection
HKL-2000data scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-09-12
    Type: Initial release
  • Version 1.1: 2008-05-01
    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, Refinement description