5DV7

Crystal Structure of NF90 tandem dsRBDs with dsRNA

• PDB DOI: https://doi.org/10.2210/pdb5DV7/pdb
• NAKB: 5DV7

• Classification: RNA BINDING PROTEIN
• Organism(s): synthetic construct, Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-09-21 Released: 2016-01-13 
• Deposition Author(s): Jayachandran, U., Grey, H., Cook, A.G.
• Funding Organization(s): Medical Research Council (United Kingdom), Wellcome Trust

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 0.273 
• R-Value Work: 0.239 
• R-Value Observed: 0.240 

Literature

Nuclear factor 90 uses an ADAR2-like binding mode to recognize specific bases in dsRNA.

Jayachandran, U., Grey, H., Cook, A.G.

(2016) Nucleic Acids Res 44: 1924-1936

• PubMed: 26712564 
• DOI: https://doi.org/10.1093/nar/gkv1508
• Primary Citation of Related Structures:  
  5DV7


• PubMed Abstract: 
  

  Nuclear factors 90 and 45 (NF90 and NF45) form a protein complex involved in the post-transcriptional control of many genes in vertebrates. NF90 is a member of the dsRNA binding domain (dsRBD) family of proteins. RNA binding partners identified so far include elements in 3' untranslated regions of specific mRNAs and several non-coding RNAs. In NF90, a tandem pair of dsRBDs separated by a natively unstructured segment confers dsRNA binding activity. We determined a crystal structure of the tandem dsRBDs of NF90 in complex with a synthetic dsRNA. This complex shows surprising similarity to the tandem dsRBDs from an adenosine-to-inosine editing enzyme, ADAR2 in complex with a substrate RNA. Residues involved in unusual base-specific recognition in the minor groove of dsRNA are conserved between NF90 and ADAR2. These data suggest that, like ADAR2, underlying sequences in dsRNA may influence how NF90 recognizes its target RNAs.

---

Organizational Affiliation: 

Wellcome Trust Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 87.52 kDa 
• Atom Count: 1,637 
• Modelled Residue Count: 173 
• Deposited Residue Count: 736 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin enhancer-binding factor 3	C	700	Mus musculus	Mutation(s): 0  Gene Names: Ilf3
UniProt
Find proteins for Q9Z1X4 (Mus musculus) Explore Q9Z1X4  Go to UniProtKB:  Q9Z1X4

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*CP*CP*AP*GP*CP*AP*UP*UP*AP*UP*GP*AP*AP*AP*GP*UP*GP*A)-3')	A	18	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*UP*CP*AP*CP*UP*UP*UP*CP*AP*UP*AP*AP*UP*GP*CP*UP*GP*G)-3')	B	18	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 0.273 
• R-Value Work: 0.239 
• R-Value Observed: 0.240 
• Space Group: P 3₁ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.104	α = 90
b = 100.104	β = 90
c = 108.007	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-01-13 
Deposition Author(s): Jayachandran, U., Grey, H., Cook, A.G.

---

Funding Organization	Location	Grant Number
Medical Research Council (United Kingdom)	United Kingdom	G1000520/1
Wellcome Trust	United Kingdom	092076

Revision History  

• Version 1.0: 2016-01-13
  Type: Initial release
  
• Version 1.1: 2016-03-09
  Changes: Database references
• Version 1.2: 2017-09-13
  Changes: Author supporting evidence, Derived calculations
• Version 1.3: 2024-01-10
  Changes: Data collection, Database references, Refinement description