2OZB

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.4 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: 10.1126/science.1137924

  • 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 nucle ...

    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

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
U4/U6.U5 tri-snRNP 15.5 kDa protein
A, D
130Homo sapiensMutation(s): 0 
Gene Names: SNU13 (NHP2L1)
Find proteins for P55769 (Homo sapiens)
Go to Gene View: SNU13
Go to UniProtKB:  P55769
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
U4/U6 small nuclear ribonucleoprotein Prp31
B, E
260Homo sapiensMutation(s): 0 
Gene Names: PRPF31 (PRP31)
Find proteins for Q8WWY3 (Homo sapiens)
Go to Gene View: PRPF31
Go to UniProtKB:  Q8WWY3
Entity ID: 1
MoleculeChainsLengthOrganism
RNA comprising the 5' Stem-Loop RNA of U4snRNAC,F33N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA
Download SDF File 
Download CCD File 
A, B, E
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 83.555α = 90.00
b = 99.896β = 90.00
c = 169.645γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
MAR345data collection
DENZOdata reduction
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-03-20
    Type: Initial release
  • Version 1.1: 2008-01-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description
  • Version 1.4: 2018-01-24
    Type: Data collection