4ZLD

Crystal structure of human Roquin-2 ROQ domain in complex with Roquin CDE RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 

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This is version 1.2 of the entry. See complete history


Literature

Structure of human Roquin-2 and its complex with constitutive-decay element RNA

Sakurai, S.Ohto, U.Shimizu, T.

(2015) Acta Crystallogr F Struct Biol Commun 71: 1048-1054

  • DOI: https://doi.org/10.1107/S2053230X15011887
  • Primary Citation of Related Structures:  
    4ZLC, 4ZLD

  • PubMed Abstract: 

    Roquin mediates mRNA degradation by recognizing the constitutive-decay element (CDE) in the 3' untranslated region of the target gene followed by recruitment of the deadenylation machinery. Deficiency or dysfunction of Roquin has been associated with autoimmunity and inflammation. To establish the structural basis for the recognition of CDE RNA by Roquin, the crystal structure of the ROQ domain of human Roquin-2 was determined in ligand-free and CDE-derived RNA-bound forms. The ROQ domain of Roquin-2 folded into a winged-helix structure in which the wing region showed structural flexibility and acted as a lid for RNA binding. The CDE RNA, forming a stem-loop structure, bound to the positively charged surface of the ROQ domain and was mainly recognized via direct interactions with the phosphate backbone in the 5' half of the stem-loop and its triloop and via indirect water-mediated interactions. Structural comparison with Roquin-1 revealed conserved features of the RNA-binding mode. Therefore, it is suggested that the Roquin proteins function redundantly in mRNA degradation.


  • Organizational Affiliation

    Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Roquin-2155Homo sapiensMutation(s): 0 
Gene Names: RC3H2MNABRNF164
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HBD1 (Homo sapiens)
Explore Q9HBD1 
Go to UniProtKB:  Q9HBD1
PHAROS:  Q9HBD1
GTEx:  ENSG00000056586 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HBD1
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (5'-R(*UP*AP*AP*CP*UP*UP*CP*UP*GP*UP*GP*AP*AP*GP*UP*UP*G)-3')17Homo sapiens
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.236α = 90
b = 89.955β = 90
c = 84.632γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science KAKENHIJapan26711002
Japan Society for the Promotion of Science KAKENHIJapan25291010

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-19
    Type: Initial release
  • Version 1.1: 2020-02-19
    Changes: Data collection, Derived calculations
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references