5ELH

Crystal structure of mouse Unkempt zinc fingers 1-3 (ZnF1-3), bound to RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Recognition of distinct RNA motifs by the clustered CCCH zinc fingers of neuronal protein Unkempt.

Murn, J.Teplova, M.Zarnack, K.Shi, Y.Patel, D.J.

(2016) Nat.Struct.Mol.Biol. 23: 16-23

  • DOI: 10.1038/nsmb.3140
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Unkempt is an evolutionarily conserved RNA-binding protein that regulates translation of its target genes and is required for the establishment of the early bipolar neuronal morphology. Here we determined the X-ray crystal structure of mouse Unkempt ...

    Unkempt is an evolutionarily conserved RNA-binding protein that regulates translation of its target genes and is required for the establishment of the early bipolar neuronal morphology. Here we determined the X-ray crystal structure of mouse Unkempt and show that its six CCCH zinc fingers (ZnFs) form two compact clusters, ZnF1-3 and ZnF4-6, that recognize distinct trinucleotide RNA substrates. Both ZnF clusters adopt a similar overall topology and use distinct recognition principles to target specific RNA sequences. Structure-guided point mutations reduce the RNA binding affinity of Unkempt both in vitro and in vivo, ablate Unkempt's translational control and impair the ability of Unkempt to induce a bipolar cellular morphology. Our study unravels a new mode of RNA sequence recognition by clusters of CCCH ZnFs that is critical for post-transcriptional control of neuronal morphology.


    Organizational Affiliation

    Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RING finger protein unkempt homolog
A, B
145Mus musculusMutation(s): 0 
Gene Names: Unk (Kiaa1753, Zc3h5, Zc3hdc5)
Find proteins for Q8BL48 (Mus musculus)
Go to UniProtKB:  Q8BL48
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(*UP*UP*AP*UP*U)-3')R5Mus musculus
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.178 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 43.194α = 90.00
b = 56.559β = 90.00
c = 131.025γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
XDSdata reduction
PHENIXrefinement
AutoSolphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM104962

Revision History 

  • Version 1.0: 2015-12-09
    Type: Initial release
  • Version 1.1: 2015-12-23
    Type: Database references
  • Version 1.2: 2016-01-20
    Type: Database references
  • Version 1.3: 2017-09-27
    Type: Author supporting evidence, Derived calculations