6K6U

Crystal structure of the human YTHDC2 YTH domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 

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This is version 1.1 of the entry. See complete history


Literature

Crystal structure of human YTHDC2 YTH domain.

Ma, C.Liao, S.Zhu, Z.

(2019) Biochem Biophys Res Commun 518: 678-684

  • DOI: https://doi.org/10.1016/j.bbrc.2019.08.107
  • Primary Citation of Related Structures:  
    6K6U

  • PubMed Abstract: 

    N 6 -methyladenosine (m 6 A) "readers" play an important role in mRNA functions and metabolism. YTHDC2, as one of the m 6 A readers, controls fertileness through decreasing associated mRNA abundance and enhancing the translation efficiency of related mRNA via binding the targeted m 6 A RNA. However, how YTH domain of YTHDC2 recognize m 6 A RNA is still unknown. In this study, we determined the crystal structure of human YTHDC2 YTH domain, which adopts similar architecture to other solved YTH domain structures. YTHDC2 contains a conserved m 6 A binding pocket, and similar RNA binding surface shared by YTHDC1.


  • Organizational Affiliation

    Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, 230027, Hefei, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3'-5' RNA helicase YTHDC2
A, B
143Homo sapiensMutation(s): 0 
Gene Names: YTHDC2
EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H6S0 (Homo sapiens)
Explore Q9H6S0 
Go to UniProtKB:  Q9H6S0
PHAROS:  Q9H6S0
GTEx:  ENSG00000047188 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H6S0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.52α = 90
b = 49.52β = 90
c = 119.05γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina--

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-25
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description