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: 2.6 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Arabidopsis JMJ13
A
490Arabidopsis thalianaMutation(s): 0 
Gene Names: MQD22.4 (MQD22_4)
Find proteins for F4KIX0 (Arabidopsis thaliana)
Go to UniProtKB:  F4KIX0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H3.2
B
12Arabidopsis thalianaMutation(s): 0 
Gene Names: HTR2, HTR3, HTR13, HTR9, HTR1
Find proteins for P59226 (Arabidopsis thaliana)
Go to UniProtKB:  P59226
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.213 
  • Space Group: P 62 2 2
Unit Cell:
Length (Å)Angle (°)
a = 128.794α = 90.00
b = 128.794β = 90.00
c = 230.642γ = 120.00
Software Package:
Software NamePurpose
HKL-3000data scaling
HKL-3000data reduction
PHENIXrefinement
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



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