5XEG

The structure of OsALKBH1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.164 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Identification and analysis of adenine N6-methylation sites in the rice genome.

Zhou, C.Wang, C.Liu, H.Zhou, Q.Liu, Q.Guo, Y.Peng, T.Song, J.Zhang, J.Chen, L.Zhao, Y.Zeng, Z.Zhou, D.X.

(2018) Nat Plants 4: 554-563

  • DOI: 10.1038/s41477-018-0214-x
  • Primary Citation of Related Structures:  
    5XEG, 5XOI

  • PubMed Abstract: 
  • DNA N 6 -methyladenine (6mA) is a non-canonical DNA modification that is present at low levels in different eukaryotes 1-8 , but its prevalence and genomic function in higher plants are unclear. Using mass spectrometry, immunoprecip ...

    DNA N 6 -methyladenine (6mA) is a non-canonical DNA modification that is present at low levels in different eukaryotes 1-8 , but its prevalence and genomic function in higher plants are unclear. Using mass spectrometry, immunoprecipitation and validation with analysis of single-molecule real-time sequencing, we observed that about 0.2% of all adenines are 6mA methylated in the rice genome. 6mA occurs most frequently at GAGG motifs and is mapped to about 20% of genes and 14% of transposable elements. In promoters, 6mA marks silent genes, but in bodies correlates with gene activity. 6mA overlaps with 5-methylcytosine (5mC) at CG sites in gene bodies and is complementary to 5mC at CHH sites in transposable elements. We show that OsALKBH1 may be potentially involved in 6mA demethylation in rice. The results suggest that 6mA is complementary to 5mC as an epigenomic mark in rice and reinforce a distinct role for 6mA as a gene expression-associated epigenomic mark in eukaryotes.


    Organizational Affiliation

    Institute of Plant Science of Paris-Saclay (IPS2), CNRS, INRA, Université Paris-sud 11, Université Paris-Saclay, Orsay, France. dao-xiu.zhou@u-psud.fr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Oxidoreductase, 2OG-Fe oxygenase family protein, putative, expressed A231Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: LOC_Os03g60190OsJ_13105
Find proteins for Q10BI6 (Oryza sativa subsp. japonica)
Explore Q10BI6 
Go to UniProtKB:  Q10BI6
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AKG
Query on AKG

Download Ideal Coordinates CCD File 
A
2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.164 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.15α = 90
b = 67.729β = 99.89
c = 67.967γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-06-13
    Type: Initial release
  • Version 1.1: 2018-12-19
    Changes: Data collection, Database references