Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 2-mer - A2 Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 83.40 kDa 
• Atom Count: 4770 
• Residue Count: 640 
• Unique protein chains: 2

4AT9

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

• DOI: 10.2210/pdb4AT9/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2012-05-05 Released: 2012-08-01 
• Deposition Author(s): Wolkowicz, U.M., Cook, A.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.263 
• R-Value Work: 0.236 
• R-Value Observed: 0.237 

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

• PubMed: 22833610 
• DOI: 10.1093/nar/gks696
• Primary Citation of Related Structures:  
  4ATB, 4AT7, 4AT8, 4AT9


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
INTERLEUKIN ENHANCER-BINDING FACTOR 2	A	364	Mus musculus	Mutation(s): 0  Gene Names: Ilf2, Nf45
Find proteins for Q9CXY6 (Mus musculus) Explore Q9CXY6  Go to UniProtKB:  Q9CXY6

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
INTERLEUKIN ENHANCER-BINDING FACTOR 3	B	383	Mus musculus	Mutation(s): 0  Gene Names: Ilf3
Find proteins for Q9Z1X4 (Mus musculus) Explore Q9Z1X4  Go to UniProtKB:  Q9Z1X4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UTP	A	URIDINE 5'-TRIPHOSPHATE C9 H15 N2 O15 P3 PGAVKCOVUIYSFO-XVFCMESISA-N
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.263 
• R-Value Work: 0.236 
• R-Value Observed: 0.237 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.849	α = 90
b = 133.516	β = 90
c = 177.983	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-05-05 
• Released Date: 2012-08-01 
Deposition Author(s): Wolkowicz, U.M., Cook, A.G.

Revision History 

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