3X1O | pdb_00003x1o

Crystal structure of the ROQ domain of human Roquin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.252 (Depositor), 0.255 (DCC) 
  • R-Value Work: 
    0.217 (Depositor), 0.221 (DCC) 
  • R-Value Observed: 
    0.219 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3X1O

This is version 1.1 of the entry. See complete history

Literature

Roquin binds microRNA-146a and Argonaute2 to regulate microRNA homeostasis

Srivastava, M.Duan, G.Kershaw, N.J.Athanasopoulos, V.Yeo, J.H.Ose, T.Hu, D.Brown, S.H.J.Jergic, S.Patel, H.R.Pratama, A.Richards, S.Verma, A.Jones, E.Y.Heissmeyer, V.Preiss, T.Dixon, N.E.Chong, M.M.W.Babon, J.J.Vinuesa, C.G.

(2015) Nat Commun 6: 6253-6253

  • DOI: https://doi.org/10.1038/ncomms7253
  • Primary Citation Related Structures: 
    3X1O

  • PubMed Abstract: 

    Roquin is an RNA-binding protein that prevents autoimmunity and inflammation via repression of bound target mRNAs such as inducible costimulator (Icos). When Roquin is absent or mutated (Roquin(san)), Icos is overexpressed in T cells. Here we show that Roquin enhances Dicer-mediated processing of pre-miR-146a. Roquin also directly binds Argonaute2, a central component of the RNA-induced silencing complex, and miR-146a, a microRNA that targets Icos mRNA. In the absence of functional Roquin, miR-146a accumulates in T cells. Its accumulation is not due to increased transcription or processing, rather due to enhanced stability of mature miR-146a. This is associated with decreased 3' end uridylation of the miRNA. Crystallographic studies reveal that Roquin contains a unique HEPN domain and identify the structural basis of the 'san' mutation and Roquin's ability to bind multiple RNAs. Roquin emerges as a protein that can bind Ago2, miRNAs and target mRNAs, to control homeostasis of both RNA species.


  • Organizational Affiliation
    • Department of Pathogens and Immunity, John Curtin School of Medical Research, Canberra, Australian Capital Territory 2601, Australia.

Macromolecule Content 

  • Total Structure Weight: 50.21 kDa 
  • Atom Count: 2,519 
  • Modeled Residue Count: 299 
  • Deposited Residue Count: 416 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Roquin-1
A, B
208Homo sapiensMutation(s): 0 
Gene Names: RC3H1KIAA2025RNF198
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q5TC82 (Homo sapiens)
Explore Q5TC82 
Go to UniProtKB:  Q5TC82
PHAROS:  Q5TC82
GTEx:  ENSG00000135870 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5TC82
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IOD

Query on IOD



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.252 (Depositor), 0.255 (DCC) 
  • R-Value Work:  0.217 (Depositor), 0.221 (DCC) 
  • R-Value Observed: 0.219 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.003α = 90
b = 78.322β = 90
c = 184.075γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
SOLVEphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-11
    Type: Initial release
  • Version 1.1: 2024-03-20
    Changes: Data collection, Database references, Derived calculations