6IP4

Crystal structure of Arabidopsis thaliana JMJ13 catalytic domain in complex with NOG and an H3K27me3 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 

wwPDB Validation 3D Report Full Report



Literature

The Arabidopsis H3K27me3 demethylase JUMONJI 13 is a temperature and photoperiod dependent flowering repressor.

Zheng, S.Hu, H.Ren, H.Yang, Z.Qiu, Q.Qi, W.Liu, X.Chen, X.Cui, X.Li, S.Zhou, B.Sun, D.Cao, X.Du, J.

(2019) Nat Commun 10: 1303-1303

  • DOI: 10.1038/s41467-019-09310-x
  • Primary Citation of Related Structures:  
    6IP0, 6IP4

  • PubMed Abstract: 
  • In plants, flowering time is controlled by environmental signals such as day-length and temperature, which regulate the floral pathway integrators, including FLOWERING LOCUS T (FT), by genetic and epigenetic mechanisms. Here, we identify an H3K27me3 ...

    In plants, flowering time is controlled by environmental signals such as day-length and temperature, which regulate the floral pathway integrators, including FLOWERING LOCUS T (FT), by genetic and epigenetic mechanisms. Here, we identify an H3K27me3 demethylase, JUMONJI 13 (JMJ13), which regulates flowering time in Arabidopsis. Structural characterization of the JMJ13 catalytic domain in complex with its substrate peptide reveals that H3K27me3 is specifically recognized through hydrogen bonding and hydrophobic interactions. Under short-day conditions, the jmj13 mutant flowers early and has increased FT expression at high temperatures, but not at low temperatures. In contrast, jmj13 flowers early in long-day conditions regardless of temperature. Long-day condition and higher temperature induce the expression of JMJ13 and increase accumulation of JMJ13. Together, our data suggest that the H3K27me3 demethylase JMJ13 acts as a temperature- and photoperiod-dependent flowering repressor.


    Organizational Affiliation

    Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China. jmdu@sibs.ac.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Arabidopsis JMJ13A490Arabidopsis thalianaMutation(s): 0 
Gene Names: MQD22.4MQD22_4At5g46910
Find proteins for F4KIX0 (Arabidopsis thaliana)
Explore F4KIX0 
Go to UniProtKB:  F4KIX0
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.2B12Arabidopsis thalianaMutation(s): 0 
Gene Names: 
Find proteins for P59226 (Arabidopsis thaliana)
Explore P59226 
Go to UniProtKB:  P59226
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OGA
Query on OGA

Download CCD File 
A
N-OXALYLGLYCINE
C4 H5 N O5
BIMZLRFONYSTPT-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L
BL-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 
  • Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.794α = 90
b = 128.794β = 90
c = 230.642γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2018-11-02 
  • Released Date: 2019-04-10 
  • Deposition Author(s): Hu, H., Du, J.

Revision History 

  • Version 1.0: 2019-04-10
    Type: Initial release