1E7K

Crystal structure of the spliceosomal 15.5kD protein bound to a U4 snRNA fragment

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.216 

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


Literature

Crystal Structure of the Spliceosomal 15.5Kd Protein Bound to a U4 Snrna Fragment

Vidovic, I., Nottrott, S., Hartmuth, K., Luhrmann, R., Ficner, R.

(2000) Mol Cell 6: 1331

  • DOI: 10.1016/s1097-2765(00)00131-3
  • Primary Citation of Related Structures:  
    1E7K

  • PubMed Abstract: 

    • We have determined the crystal structure of a spliceosomal RNP complex comprising the 15.5kD protein of the human U4/U6.U5 tri-snRNP and the 5' stem-loop of U4 snRNA. The protein interacts almost exclusively with a purine-rich (5+2) internal loop within the 5' stem-loop, giving an unusual RNA fold characterized by two tandem sheared G-A base pairs, a high degree of purine stacking, and the accommodation of a single RNA base, rotated out of the RNA chain, in a pocket of the protein ...

    We have determined the crystal structure of a spliceosomal RNP complex comprising the 15.5kD protein of the human U4/U6.U5 tri-snRNP and the 5' stem-loop of U4 snRNA. The protein interacts almost exclusively with a purine-rich (5+2) internal loop within the 5' stem-loop, giving an unusual RNA fold characterized by two tandem sheared G-A base pairs, a high degree of purine stacking, and the accommodation of a single RNA base, rotated out of the RNA chain, in a pocket of the protein. Apart from yielding the structure of an important entity in the pre-mRNA splicing apparatus, this work also implies a model for the complex of the 15.5kD protein with box C/D snoRNAs. It additionally suggests a general recognition principle in a novel family of RNA binding proteins.

    Related Citations: 
    • Functional Interaction of a Novel 15.5Kd [U4/U6.U5] Tri-Snrnp Protein with the 5' Stem-Loop of U4 Snrna
      Nottrott, S., Hartmuth, K., Fabrizio, P., Urlaub, H., Vidovic, I., Ficner, R., Luhrmann, R.
      (1999) EMBO J 18: 6119
    Organizational Affiliation: 

    Institut für Molekularbiologie und Tumorforschung, Philipps-Universität Marburg, Emil-Mannkopff-Strasse 2, 35037 Marburg, Germany.



Macromolecules

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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
15.5 KD RNA BINDING PROTEINA, B128Homo sapiensMutation(s): 0 
Gene Names: SNU13, NHP2L1
Find proteins for P55769 (Homo sapiens)
Explore P55769 
Go to UniProtKB:  P55769
NIH Common Fund Data Resources
PHAROS:  P55769
GTEx:  ENSG00000100138
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
RNA (5'-R(*GP*CP*CP*AP*AP*UP*GP*AP*GP*GP*UP*UP*UP* AP*UP*CP*CP*GP*AP*GP*G*C(-3')C, D22Homo sapiens
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.216 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.756α = 90
b = 55.287β = 90
c = 146.735γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement
SHARPphasing
SOLOMONphasing
SOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-02-19
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance