Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 27.83 kDa 
• Atom Count: 1592 
• Modelled Residue Count: 184 
• Deposited Residue Count: 220 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

4JVH

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

• PDB DOI: 10.2210/pdb4JVH/pdb
• NDB: NA2330

• Classification: RNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-03-25 Released: 2013-05-08 
• Deposition Author(s): Teplova, M., Hafner, M., Teplov, D., Essig, K., Tuschl, T., Patel, D.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 0.316 
• R-Value Work: 0.243 
• R-Value Observed: 0.250 

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

• PubMed: 23630077 
• DOI: 10.1101/gad.216531.113
• Primary Citation of Related Structures:  
  4JVH, 4JVY


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein quaking	A	209	Homo sapiens	Mutation(s): 0  Gene Names: QKI, HKQ
UniProt & NIH Common Fund Data Resources
Find proteins for Q96PU8 (Homo sapiens) Explore Q96PU8  Go to UniProtKB:  Q96PU8
PHAROS:  Q96PU8 GTEx:  ENSG00000112531

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*UP*UP*CP*AP*CP*UP*AP*AP*CP*AP*A)-3')	B [auth D]	11	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 0.316 
• R-Value Work: 0.243 
• R-Value Observed: 0.250 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.634	α = 90
b = 98.634	β = 90
c = 103.137	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-03-25 
• Released Date: 2013-05-08 
Deposition Author(s): Teplova, M., Hafner, M., Teplov, D., Essig, K., Tuschl, T., Patel, D.J.

Revision History  

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