4Z31

Crystal structure of the RC3H2 ROQ domain in complex with stem-loop and double-stranded forms of RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.245 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

New Insights into the RNA-Binding and E3 Ubiquitin Ligase Activities of Roquins.

Zhang, Q.Fan, L.Hou, F.Dong, A.Wang, Y.X.Tong, Y.

(2015) Sci Rep 5: 15660-15660

  • DOI: 10.1038/srep15660
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Roquins are a family of highly conserved RNA-binding proteins that also contain a RING-type E3 ubiquitin ligase domain. They repress constitutive decay elements containing mRNAs and play a critical role in RNA homeostasis and immunological self-toler ...

    Roquins are a family of highly conserved RNA-binding proteins that also contain a RING-type E3 ubiquitin ligase domain. They repress constitutive decay elements containing mRNAs and play a critical role in RNA homeostasis and immunological self-tolerance. Here we present the crystal structures of the RNA-binding region of Roquin paralog RC3H2 in both apo- and RNA-bound forms. The RNA-binding region has a bipartite architecture composed of ROQ and HEPN domains, and can bind to stem-loop and double-stranded RNAs simultaneously. The two domains undergo a large orientation change to accommodate RNA duplex binding. We profiled E2 ubiquitin-conjugating enzymes that pair with Roquins and found that RC3H1 and RC3H2 interact with two sets of overlapping but not identical E2 enzymes to drive the assembly of polyubiquitin chains of different linkages. Crystal structures, small-angle X-ray scattering, and E2 profiling revealed that while the two paralogs are highly homologous, RC3H2 and RC3H1 are different in their structures and functions. We also demonstrated that RNA duplex binding to RC3H2 cross-talks with its E3 ubiquitin ligase function using an in vitro auto-ubiquitination assay.


    Organizational Affiliation

    Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Roquin-2
A, B
319Homo sapiensMutation(s): 0 
Gene Names: RC3H2 (MNAB, RNF164)
EC: 2.3.2.27
Find proteins for Q9HBD1 (Homo sapiens)
Go to Gene View: RC3H2
Go to UniProtKB:  Q9HBD1
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(*A)-D(P*UP*GP*UP*UP*CP*UP*GP*UP*GP*AP*AP*CP*AP*C)-3')C,D,E,F15Homo sapiens
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

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Download CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
UNX
Query on UNX

Download SDF File 
Download CCD File 
A
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.245 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 60.299α = 90.00
b = 174.734β = 114.12
c = 61.290γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data scaling
PDB_EXTRACTdata extraction
PHASERphasing
REFMACrefinement
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-10-14
    Type: Initial release
  • Version 1.1: 2016-06-29
    Type: Database references