4QI2 | pdb_00004qi2

X-ray structure of the ROQ domain from murine Roquin-1 in complex with a 23-mer Tnf-CDE RNA

• PDB DOI: https://doi.org/10.2210/pdb4QI2/pdb
• NAKB: 4QI2

• Classification: RNA BINDING PROTEIN/RNA
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-05-30 Released: 2014-07-16 
• Deposition Author(s): Janowski, R., Schlundt, A., Sattler, M., Niessing, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.247 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

Literature

Structural basis for RNA recognition in roquin-mediated post-transcriptional gene regulation.

Schlundt, A., Heinz, G.A., Janowski, R., Geerlof, A., Stehle, R., Heissmeyer, V., Niessing, D., Sattler, M.

(2014) Nat Struct Mol Biol 21: 671-678

• PubMed: 25026077 
• DOI: https://doi.org/10.1038/nsmb.2855
• Primary Citation Related Structures: 
  4QI0, 4QI2


• PubMed Abstract: 
  

  Roquin function in T cells is essential for the prevention of autoimmune disease. Roquin interacts with the 3' untranslated regions (UTRs) of co-stimulatory receptors and controls T-cell activation and differentiation. Here we show that the N-terminal ROQ domain from mouse roquin adopts an extended winged-helix (WH) fold, which is sufficient for binding to the constitutive decay element (CDE) in the Tnf 3' UTR. The crystal structure of the ROQ domain in complex with a prototypical CDE RNA stem-loop reveals tight recognition of the RNA stem and its triloop. Surprisingly, roquin uses mainly non-sequence-specific contacts to the RNA, thus suggesting a relaxed CDE consensus and implicating a broader spectrum of target mRNAs than previously anticipated. Consistently with this, NMR and binding experiments with CDE-like stem-loops together with cell-based assays confirm roquin-dependent regulation of relaxed CDE consensus motifs in natural 3' UTRs.

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Organizational Affiliation: 
• 1] Biomolecular NMR Spectroscopy, Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany. [2] Center for Integrated Protein Science Munich at Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Garching, Germany. [3].
1] Institute of Molecular Immunology, Research Unit Molecular Immune Regulation, Helmholtz Zentrum München, Germany. [2] Institute for Immunology, Ludwig-Maximilians-Universität München, Munich, Germany. [3].
1] Group Intracellular Transport and RNA Biology, Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany. [2].
Biomolecular NMR Spectroscopy, Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.
Center for Integrated Protein Science Munich at Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Garching, Germany.
1] Institute of Molecular Immunology, Research Unit Molecular Immune Regulation, Helmholtz Zentrum München, Germany. [2] Institute for Immunology, Ludwig-Maximilians-Universität München, Munich, Germany.
Group Intracellular Transport and RNA Biology, Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.
1] Biomolecular NMR Spectroscopy, Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany. [2] Center for Integrated Protein Science Munich at Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Garching, Germany.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 111.67 kDa 
• Atom Count: 6,546 
• Modeled Residue Count: 686 
• Deposited Residue Count: 812 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Roquin-1	A, B, C, D	180	Mus musculus	Mutation(s): 0  Gene Names: Gm551, Kiaa2025, Rc3h1 EC: 2.3.2.27
UniProt
Find proteins for Q4VGL6 (Mus musculus) Explore Q4VGL6  Go to UniProtKB:  Q4VGL6

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*AP*CP*AP*UP*GP*UP*UP*UP*UP*CP*UP*GP*UP*GP*AP*AP*AP*AP*CP*GP*GP*AP*G)-3')	E, F, G, H	23	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.247 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.56	α = 105.68
b = 60.41	β = 101.36
c = 84.37	γ = 95.72

Software Package:

Software Name	Purpose
DNA	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-16 
Deposition Author(s): Janowski, R., Schlundt, A., Sattler, M., Niessing, D.

Revision History  

• Version 1.0: 2014-07-16
  Type: Initial release
  
• Version 1.1: 2014-08-20
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Refinement description