2OZB

Structure of a human Prp31-15.5K-U4 snRNA complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history. 


Literature

Binding of the human Prp31 Nop domain to a composite RNA-protein platform in U4 snRNP.

Liu, S., Li, P., Dybkov, O., Nottrott, S., Hartmuth, K., Luhrmann, R., Carlomagno, T., Wahl, M.C.

(2007) Science 316: 115-120

  • DOI: https://doi.org/10.1126/science.1137924
  • Primary Citation of Related Structures:  
    2OZB

  • PubMed Abstract: 

    Although highly homologous, the spliceosomal hPrp31 and the nucleolar Nop56 and Nop58 (Nop56/58) proteins recognize different ribonucleoprotein (RNP) particles. hPrp31 interacts with complexes containing the 15.5K protein and U4 or U4atac small nuclear RNA (snRNA), whereas Nop56/58 associate with 15.5K-box C/D small nucleolar RNA complexes. We present structural and biochemical analyses of hPrp31-15.5K-U4 snRNA complexes that show how the conserved Nop domain in hPrp31 maintains high RNP binding selectivity despite relaxed RNA sequence requirements. The Nop domain is a genuine RNP binding module, exhibiting RNA and protein binding surfaces. Yeast two-hybrid analyses suggest a link between retinitis pigmentosa and an aberrant hPrp31-hPrp6 interaction that blocks U4/U6-U5 tri-snRNP formation.

    • Organizational Affiliation: 

    Abteilung Zelluläre Biochemie, Max-Planck-Institut für Biophysikalische Chemie, Am Fassberg 11, D-37077 Göttingen, Germany.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
U4/U6.U5 tri-snRNP 15.5 kDa proteinC [auth A],
E [auth D]		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
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
U4/U6 small nuclear ribonucleoprotein Prp31D [auth B],
F [auth E]		260Homo sapiensMutation(s): 0 
Gene Names: PRPF31, PRP31
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
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Entity ID: 1
MoleculeChains LengthOrganismImage
RNA comprising the 5' Stem-Loop RNA of U4snRNAA [auth C],
B [auth F]		33N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.555α = 90
b = 99.896β = 90
c = 169.645γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-03-20
    Type: Initial release
  • Version 1.1: 2008-01-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2018-01-24
    Changes: Data collection
  • Version 1.5: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description