5DV7

Crystal Structure of NF90 tandem dsRBDs with dsRNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.239 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • DOI: 10.1093/nar/gkv1508

  • 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 fa ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Interleukin enhancer-binding factor 3
C
700Mus musculusMutation(s): 0 
Gene Names: Ilf3
Find proteins for Q9Z1X4 (Mus musculus)
Go to UniProtKB:  Q9Z1X4
Entity ID: 1
MoleculeChainsLengthOrganism
RNA (5'-R(*CP*CP*AP*GP*CP*AP*UP*UP*AP*UP*GP*AP*AP*AP*GP*UP*GP*A)-3')A18synthetic construct
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(*UP*CP*AP*CP*UP*UP*UP*CP*AP*UP*AP*AP*UP*GP*CP*UP*GP*G)-3')B18synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.239 
  • Space Group: P 31 1 2
Unit Cell:
Length (Å)Angle (°)
a = 100.104α = 90.00
b = 100.104β = 90.00
c = 108.007γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomG1000520/1
Wellcome TrustUnited Kingdom092076

Revision History 

  • Version 1.0: 2016-01-13
    Type: Initial release
  • Version 1.1: 2016-03-09
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Author supporting evidence, Derived calculations