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 
  • R-Value Observed: 0.158 

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This is version 1.5 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: https://doi.org/10.1016/j.bbrc.2017.09.145
  • Primary Citation of Related Structures:  
    4LG8

  • 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-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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 19354Homo sapiensMutation(s): 1 
Gene Names: PRPF19, NMP200, PRP19, SNEV
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UMS4 (Homo sapiens)
Explore Q9UMS4 
Go to UniProtKB:  Q9UMS4
PHAROS:  Q9UMS4
GTEx:  ENSG00000110107 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UMS4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA
Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]		SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
UNX
Query on UNX
Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A]
UNKNOWN ATOM OR ION
X
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.055α = 90
b = 83.055β = 90
c = 75.533γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-08-07
    Type: Initial release
  • Version 1.1: 2014-01-22
    Changes: Structure summary
  • Version 1.2: 2017-05-10
    Changes: Database references, Structure summary
  • Version 1.3: 2017-11-15
    Changes: Refinement description
  • Version 1.4: 2018-01-03
    Changes: Database references
  • Version 1.5: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description