9M4R | pdb_00009m4r

crystal structure of Arabidopsis thaliana ING1 PHD finger in complex with an H3K4me3 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.200 (Depositor), 0.216 (DCC) 
  • R-Value Work: 
    0.157 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 
    0.159 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

A pair of readers of histone H3K4 methylation recruit Polycomb repressive complex 2 to regulate photoperiodic flowering.

Luo, X.Li, X.Chen, Z.Tian, S.Liu, Y.Shang, Z.Chen, L.Sun, Y.Du, J.He, Y.

(2025) Nat Commun 16: 9376-9376

  • DOI: https://doi.org/10.1038/s41467-025-64419-6
  • Primary Citation of Related Structures:  
    9M4R, 9M4S

  • PubMed Abstract: 

    The transition from vegetative growth to reproduction in flowering plants is often timed by seasonal changes in day length (photoperiod). In the long-day (LD) plant Arabidopsis thaliana, the photoperiod pathway induces a daily rhythmic activation of the florigen gene FLOWERING LOCUS T (FT) to promote the floral transition. Under inductive LDs, FT expression is activated around dusk, but to be repressed overnight and into the early afternoon the next day. Here, we report that AtING1 and AtING2, Arabidopsis homologs of the mammalian Inhibitor of Growth (ING) proteins, read di- and tri-methylated histone-3 lysine 4 (H3K4me2/me3) on FT chromatin and further recruit Polycomb-repressive complex 2 (PRC2) to repress FT expression at night and into the early afternoon the next day, following FT activation at dusk. This prevents precocious flowering under inductive LDs. Our study reveals that the H3K4me2/me3-ING1/2-PRC2 module timely represses FT expression following the daily rhythmic FT activation, to prevent excessive FT expression and thus precisely control flowering time, in response to inductive photoperiodic signals.


  • Organizational Affiliation
    • Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Shandong, China. xiao.luo@pku-iaas.edu.cn.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PHD finger protein ING173Arabidopsis thalianaMutation(s): 0 
Gene Names: ING1At3g24010F14O13.20
UniProt
Find proteins for Q9LIQ6 (Arabidopsis thaliana)
Explore Q9LIQ6 
Go to UniProtKB:  Q9LIQ6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9LIQ6
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.1B [auth P]10Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P59226 (Arabidopsis thaliana)
Explore P59226 
Go to UniProtKB:  P59226
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP59226
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
M3L
Query on M3L
B [auth P]L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.200 (Depositor), 0.216 (DCC) 
  • R-Value Work:  0.157 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 0.159 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.83α = 90
b = 41.83β = 90
c = 69.435γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data scaling
HKL-3000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2025-11-05 
  • Deposition Author(s): Li, X., Du, J.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32325008

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-05
    Type: Initial release