3SIV

Structure of a hPrp31-15.5K-U4atac 5' stem loop complex, dimeric form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis for the dual U4 and U4atac snRNA-binding specificity of spliceosomal protein hPrp31.

Liu, S.Ghalei, H.Luhrmann, R.Wahl, M.C.

(2011) RNA 17: 1655-1663

  • DOI: https://doi.org/10.1261/rna.2690611
  • Primary Citation of Related Structures:  
    3SIU, 3SIV

  • PubMed Abstract: 

    Human proteins 15.5K and hPrp31 are components of the major spliceosomal U4 snRNP and of the minor spliceosomal U4atac snRNP. The two proteins bind to related 5'-stem loops (5'SLs) of the U4 and U4atac snRNAs in a strictly sequential fashion. The primary binding 15.5K protein binds at K-turns that exhibit identical sequences in the two snRNAs. However, RNA sequences contacted by the secondary binding hPrp31 differ in U4 and U4atac snRNAs, and the mechanism by which hPrp31 achieves its dual specificity is presently unknown. We show by crystal structure analysis that the capping pentaloops of the U4 and U4atac 5'SLs adopt different structures in the ternary hPrp31-15.5K-snRNA complexes. In U4atac snRNA, a noncanonical base pair forms across the pentaloop, based on which the RNA establishes more intimate interactions with hPrp31 compared with U4 snRNA. Stacking of hPrp31-His270 on the noncanonical base pair at the base of the U4atac pentaloop recapitulates intramolecular stabilizing principles known from the UUCG and GNRA families of RNA tetraloops. Rational mutagenesis corroborated the importance of the noncanonical base pair and the U4atac-specific hPrp31-RNA interactions for complex stability. The more extensive hPrp31-U4atac snRNA interactions are in line with a higher stability of the U4atac compared with the U4-based ternary complex seen in gel-shift assays, which may explain how U4atac snRNA can compete with the more abundant U4 snRNA for the same protein partners in vivo.


  • Organizational Affiliation

    Freie Universität Berlin, Fachbereich Biologie/Chemie/Pharmazie, Abteilung Strukturbiochemie, Takustraße 6, D-14195 Berlin, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NHP2-like protein 1
A, D, G, J
130Homo sapiensMutation(s): 0 
Gene Names: NHP2L1
UniProt & NIH Common Fund Data Resources
Find proteins for P55769 (Homo sapiens)
Explore P55769 
Go to UniProtKB:  P55769
PHAROS:  P55769
GTEx:  ENSG00000100138 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55769
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
U4/U6 small nuclear ribonucleoprotein Prp31
B, E, H, K
254Homo sapiensMutation(s): 0 
Gene Names: PRP31PRPF31
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WWY3 (Homo sapiens)
Explore Q8WWY3 
Go to UniProtKB:  Q8WWY3
PHAROS:  Q8WWY3
GTEx:  ENSG00000105618 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8WWY3
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains LengthOrganismImage
U4atac snRNA
C, F, I, L
32Homo sapiens
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 255.407α = 90
b = 105.325β = 127.52
c = 188.644γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-10
    Type: Initial release
  • Version 1.1: 2011-08-31
    Changes: Database references
  • Version 1.2: 2018-01-31
    Changes: Advisory, Experimental preparation
  • Version 1.3: 2023-09-13
    Changes: Advisory, Data collection, Database references, Refinement description