4AT9

Crystal structure of the NF90-NF45 dimerisation domain complex with UTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.803 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

NF45 Dimerizes with NF90, Zfr and Spnr Via a Conserved Domain that Has a Nucleotidyltransferase Fold.

Wolkowicz, U.M.Cook, A.G.

(2012) Nucleic Acids Res. 40: 9356

  • DOI: 10.1093/nar/gks696
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Nuclear factors NF90 and NF45 form a complex involved in a variety of cellular processes and are thought to affect gene expression both at the transcriptional and translational level. In addition, this complex affects the replication of several virus ...

    Nuclear factors NF90 and NF45 form a complex involved in a variety of cellular processes and are thought to affect gene expression both at the transcriptional and translational level. In addition, this complex affects the replication of several viruses through direct interactions with viral RNA. NF90 and NF45 dimerize through their common 'DZF' domain (domain associated with zinc fingers). NF90 has additional double-stranded RNA-binding domains that likely mediate its association with target RNAs. We present the crystal structure of the NF90/NF45 dimerization complex at 1.9-Å resolution. The DZF domain shows structural similarity to the template-free nucleotidyltransferase family of RNA modifying enzymes. However, both NF90 and NF45 have lost critical catalytic residues during evolution and are therefore not functional enzymes. Residues on NF90 that make up its interface with NF45 are conserved in two related proteins, spermatid perinuclear RNA-binding protein (SPNR) and zinc-finger RNA-binding protein (Zfr). Using a co-immunoprecipitation assay and site-specific mutants, we demonstrate that NF45 is also able to recognize SPNR and Zfr through the same binding interface, revealing that NF45 is able to form a variety of cellular complexes with other DZF-domain proteins.


    Organizational Affiliation

    Wellcome Trust Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Edinburgh, Midlothian EH9 3JR, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
INTERLEUKIN ENHANCER-BINDING FACTOR 2
A
364Mus musculusMutation(s): 0 
Gene Names: Ilf2 (Nf45)
Find proteins for Q9CXY6 (Mus musculus)
Go to UniProtKB:  Q9CXY6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
INTERLEUKIN ENHANCER-BINDING FACTOR 3
B
383Mus musculusMutation(s): 0 
Gene Names: Ilf3
Find proteins for Q9Z1X4 (Mus musculus)
Go to UniProtKB:  Q9Z1X4
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UTP
Query on UTP

Download SDF File 
Download CCD File 
A
URIDINE 5'-TRIPHOSPHATE
C9 H15 N2 O15 P3
PGAVKCOVUIYSFO-XVFCMESISA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.803 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.236 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 83.849α = 90.00
b = 133.516β = 90.00
c = 177.983γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PHASERphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-08-01
    Type: Initial release
  • Version 1.1: 2012-10-31
    Type: Database references
  • Version 1.2: 2018-06-20
    Type: Data collection, Derived calculations