5F5H | pdb_00005f5h

X-ray structure of Roquin ROQ domain in complex with Ox40 hexa-loop RNA motif

• PDB DOI: https://doi.org/10.2210/pdb5F5H/pdb
• NAKB: 5F5H

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


• Deposited: 2015-12-04 Released: 2016-04-06 
• Deposition Author(s): Janowski, R., Schlundt, A., Sattler, M., Niessing, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.23 Å
• R-Value Free: 
  0.257 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: experimental

Literature

Roquin recognizes a non-canonical hexaloop structure in the 3'-UTR of Ox40.

Janowski, R., Heinz, G.A., Schlundt, A., Wommelsdorf, N., Brenner, S., Gruber, A.R., Blank, M., Buch, T., Buhmann, R., Zavolan, M., Niessing, D., Heissmeyer, V., Sattler, M.

(2016) Nat Commun 7: 11032-11032

• PubMed: 27010430 
• DOI: https://doi.org/10.1038/ncomms11032
• Primary Citation Related Structures: 
  5F5F, 5F5H


• PubMed Abstract: 
  

  The RNA-binding protein Roquin is required to prevent autoimmunity. Roquin controls T-helper cell activation and differentiation by limiting the induced expression of costimulatory receptors such as tumor necrosis factor receptor superfamily 4 (Tnfrs4 or Ox40). A constitutive decay element (CDE) with a characteristic triloop hairpin was previously shown to be recognized by Roquin. Here we use SELEX assays to identify a novel U-rich hexaloop motif, representing an alternative decay element (ADE). Crystal structures and NMR data show that the Roquin-1 ROQ domain recognizes hexaloops in the SELEX-derived ADE and in an ADE-like variant present in the Ox40 3'-UTR with identical binding modes. In cells, ADE-like and CDE-like motifs cooperate in the repression of Ox40 by Roquin. Our data reveal an unexpected recognition of hexaloop cis elements for the posttranscriptional regulation of target messenger RNAs by Roquin.

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Organizational Affiliation: 
• Group Intracellular Transport and RNA Biology, Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, Neuherberg DE-85764, Germany.
Research Unit Molecular Immune Regulation, Helmholtz Zentrum München, Marchioninistrasse 25, München DE-81377, Germany.
Institute for Immunology at the Biomedical Center, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 9, Planegg-Martinsried DE-82152, Germany.
Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, Neuherberg DE-85764, Germany.
Center for Integrated Protein Science Munich at Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Lichtenbergstrasse 4, Garching DE-85747, Germany.
Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Klingelbergstrasse 50-70, Basel CH-4056, Switzerland.
AptaIT GmbH, Goethestrasse 52, München 80336, Germany.
Institute of Laboratory Animal Science, University of Zurich, Wagistrasse 12, Schlieren 8952, Switzerland.
Department of Medicine III and Transfusion Medicine, University Hospital Grosshadern, LMU, Marchioninistrasse 15, München 81377, Germany.
Department of Cell Biology at the Biomedical Center, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 9, Planegg-Martinsried DE-82152, 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)

Macromolecule Content 

• Total Structure Weight: 55.12 kDa 
• Atom Count: 3,397 
• Modeled Residue Count: 342 
• Deposited Residue Count: 404 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Roquin-1	A, B	180	Mus musculus	Mutation(s): 0  Gene Names: Rc3h1, Gm551, Kiaa2025 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(P*CP*CP*AP*CP*AP*CP*CP*GP*UP*UP*CP*UP*AP*GP*GP*UP*GP*CP*UP*GP*G)-3')	C, D	22	Mus musculus

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.23 Å
• R-Value Free:  0.257 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.66	α = 90
b = 115.79	β = 90
c = 42.61	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-04-06 
Deposition Author(s): Janowski, R., Schlundt, A., Sattler, M., Niessing, D.

Revision History  

• Version 1.0: 2016-04-06
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description