4LG8 | pdb_00004lg8

Crystal structure of PRPF19 WD40 repeats

• PDB DOI: https://doi.org/10.2210/pdb4LG8/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2013-06-27 Released: 2013-08-07 
• Deposition Author(s): Xu, C., Tempel, W., He, H., Dobrovetsky, E., Seitova, A., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 
  0.197 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.156 (Depositor), 0.169 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Models: experimental

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

• PubMed: 28962858 
• DOI: https://doi.org/10.1016/j.bbrc.2017.09.145
• Primary Citation 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.

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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.
School of Life Sciences, University of Science and Technology of China, Hefei 230027, PR China.
Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China.
High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Academy of Sciences of China, Hefei 230031, PR China.
Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada.
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.
School of Life Sciences, University of Science and Technology of China, Hefei 230027, PR China. Electronic address: [e-mail].
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. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 39.11 kDa 
• Atom Count: 2,533 
• Modeled Residue Count: 310 
• Deposited Residue Count: 354 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pre-mRNA-processing factor 19	A	354	Homo sapiens	Mutation(s): 1  Gene Names: PRPF19, NMP200, PRP19, SNEV EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UMS4 (Homo sapiens) Explore Q9UMS4  Go to UniProtKB:  Q9UMS4
PHAROS:  Q9UMS4 GTEx:  ENSG00000110107

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	B [auth A], C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
UNX	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 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.156 (Depositor), 0.169 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.055	α = 90
b = 83.055	β = 90
c = 75.533	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-07 
Deposition Author(s): Xu, C., Tempel, W., He, H., Dobrovetsky, E., Seitova, A., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

Revision History  

• 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