4JVH

Structure of the star domain of quaking protein in complex with RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.501 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.243 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structure-function studies of STAR family Quaking proteins bound to their in vivo RNA target sites.

Teplova, M.Hafner, M.Teplov, D.Essig, K.Tuschl, T.Patel, D.J.

(2013) Genes Dev. 27: 928-940

  • DOI: 10.1101/gad.216531.113
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Mammalian Quaking (QKI) and its Caenorhabditis elegans homolog, GLD-1 (defective in germ line development), are evolutionarily conserved RNA-binding proteins, which post-transcriptionally regulate target genes essential for developmental processes an ...

    Mammalian Quaking (QKI) and its Caenorhabditis elegans homolog, GLD-1 (defective in germ line development), are evolutionarily conserved RNA-binding proteins, which post-transcriptionally regulate target genes essential for developmental processes and myelination. We present X-ray structures of the STAR (signal transduction and activation of RNA) domain, composed of Qua1, K homology (KH), and Qua2 motifs of QKI and GLD-1 bound to high-affinity in vivo RNA targets containing YUAAY RNA recognition elements (RREs). The KH and Qua2 motifs of the STAR domain synergize to specifically interact with bases and sugar-phosphate backbones of the bound RRE. Qua1-mediated homodimerization generates a scaffold that enables concurrent recognition of two RREs, thereby plausibly targeting tandem RREs present in many QKI-targeted transcripts. Structure-guided mutations reduced QKI RNA-binding affinity in vitro and in vivo, and expression of QKI mutants in human embryonic kidney cells (HEK293) significantly decreased the abundance of QKI target mRNAs. Overall, our studies define principles underlying RNA target selection by STAR homodimers and provide insights into the post-transcriptional regulatory function of mammalian QKI proteins.


    Organizational Affiliation

    Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein quaking
A
209Homo sapiensMutation(s): 0 
Gene Names: QKI (HKQ)
Find proteins for Q96PU8 (Homo sapiens)
Go to Gene View: QKI
Go to UniProtKB:  Q96PU8
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(*UP*UP*CP*AP*CP*UP*AP*AP*CP*AP*A)-3')D11N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.501 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.243 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 98.634α = 90.00
b = 98.634β = 90.00
c = 103.137γ = 120.00
Software Package:
Software NamePurpose
PHENIXphasing
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-08
    Type: Initial release