4LG8

Crystal structure of PRPF19 WD40 repeats


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.156 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Crystal structure of the WD40 domain of human PRPF19.

Zhang, Y.Li, Y.Liang, X.Zhu, Z.Sun, H.He, H.Min, J.Liao, S.Liu, Y.

(2017) Biochem. Biophys. Res. Commun. 493: 1250-1253

  • DOI: 10.1016/j.bbrc.2017.09.145

  • PubMed Abstract: 
  • Human Pre-mRNA Processing factor 19 (hPRPF19) is an important component in human spliceosome machinery. hPRPF19 contains a WD40 repeats domain at its C-terminus, which is also conserved in yeast. Here we determined the crystal structure of the C-term ...

    Human Pre-mRNA Processing factor 19 (hPRPF19) is an important component in human spliceosome machinery. hPRPF19 contains a WD40 repeats domain at its C-terminus, which is also conserved in yeast. Here we determined the crystal structure of the C-terminal WD40 repeat domain of hPRPF19 by X-ray crystallography. Our structural analysis revealed some significantly different structure features between the human and yeast Prp19 WD40 repeat domain. However, there are also conserved clusters of residues at the bottom surface of the fourth and the fifth WD40 repeats, which provides the important implication for the conserved Prp19 proteins in both human and yeast.


    Organizational Affiliation

    Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China; Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada; Yunnan Provincial Key Laboratory of Entomological Biopharmaceutical R&D, Dali University, Dali 671000, PR China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing factor 19
A
354Homo sapiensMutation(s): 1 
Gene Names: PRPF19 (NMP200, PRP19, SNEV)
EC: 2.3.2.27
Find proteins for Q9UMS4 (Homo sapiens)
Go to Gene View: PRPF19
Go to UniProtKB:  Q9UMS4
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

Download SDF File 
Download CCD File 
A
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.156 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 83.055α = 90.00
b = 83.055β = 90.00
c = 75.533γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
REFMACrefinement
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-08-07
    Type: Initial release
  • Version 1.1: 2014-01-22
    Type: Structure summary
  • Version 1.2: 2017-05-10
    Type: Database references, Structure summary
  • Version 1.3: 2017-11-15
    Type: Refinement description
  • Version 1.4: 2018-01-03
    Type: Database references